
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_Samples/3164340/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-All_Samples/3215655/SKCM-All_Samples.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-All_Samples", "-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_Samples"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=211, in cluster file=288, common to both=202
[1] "Reduce the number of clustering variables from 80 to 77."
[1]  77 202
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               26               176 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               26               176 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               67               135 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               67               135 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               19               183 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               19               183 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               17               185 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               17               185 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               20               182 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               20               182 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               25               177 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               25               177 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               17               185 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               17               185 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               13               189 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               13               189 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               24               178 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               24               178 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7               195 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7               195 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               67               135 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               67               135 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16               186 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16               186 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               85               117 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               85               117 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               86               116 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               86               116 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               39               163 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               39               163 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               63               139 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               63               139 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               199 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               199 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               198 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               198 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                13                189 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                13                189 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 9                193 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 9                193 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                19                183 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                19                183 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 7                195 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 7                195 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                35                167 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                35                167 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                14                188 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                14                188 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                26                176 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                26                176 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                14                188 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                14                188 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                189 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                189 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                15                187 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                15                187 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                24                178 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                24                178 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                25                177 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                25                177 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                15                187 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                15                187 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                12                190 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                12                190 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                15                187 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                15                187 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                57                145 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                57                145 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                70                132 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                70                132 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                22                180 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                22                180 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                50                152 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                50                152 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4               198 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4               198 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               16               186 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               16               186 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                7               195 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                7               195 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               19               183 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               19               183 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               17               185 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               17               185 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               13               189 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               13               189 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               13               189 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               13               189 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               22               180 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               22               180 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               23               179 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               23               179 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               25               177 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               25               177 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               41               161 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               41               161 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               16               186 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               16               186 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               74               128 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               74               128 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               199 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               199 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               199 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               199 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               27               175 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               27               175 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                6               196 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                6               196 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              117                85 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              117                85 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               83               119 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               83               119 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                88                114 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                88                114 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               100                102 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               100                102 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                51                151 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                51                151 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                55                147 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                55                147 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                13                189 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                13                189 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                24                178 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                24                178 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                29                173 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                29                173 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                47                155 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                47                155 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                12                190 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                12                190 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                15                187 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                15                187 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                38                164 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                38                164 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                41                161 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                41                161 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                20                182 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                20                182 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                39                163 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                39                163 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                36                166 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                36                166 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                18                184 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                18                184 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                19                183 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                19                183 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                194 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                194 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                24                178 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                24                178 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                187 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                187 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               197 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5               197 
[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 202 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-A1X3 TCGA-D9-A3Z1 
          NA           NA           NA           NA           NA          122 
TCGA-D9-A3Z3 TCGA-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
          87          118         1484           NA         1555           NA 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
        1192           NA           NA         1354         1116           NA 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
          NA          680           NA          589           NA          534 
TCGA-DA-A3F8 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A299 TCGA-EB-A3HV 
         451           16           13           41           NA           39 
TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XD TCGA-EB-A3XE TCGA-EB-A3XF TCGA-EB-A3Y6 
          36            9           NA           NA            4           16 
TCGA-EB-A3Y7 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EB-A430 
          NA            8            3            6           12           NA 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
        1097          156           NA           NA         1155           NA 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
        1175          134           NA          825           NA          366 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X 
         247          269          304          197           NA           NA 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB 
          NA          769          727           NA          272           NA 
TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J 
          NA           NA           NA           NA           NA           NA 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A1A1 TCGA-ER-A3ET 
          NA           NA         1303           NA         2386          200 
TCGA-ER-A3PL TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A3YO TCGA-FR-A44A 
          52           NA          307          181           NA         2195 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZN TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A1ZT 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 
          NA           NA           NA           NA         1637           NA 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV 
         328          195            6           31            4           NA 
TCGA-GF-A2C7 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A263 TCGA-GN-A264 TCGA-GN-A265 
          NA           NA          756           NA           NA         2577 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C 
          NA           NA           NA           NA           NA           NA 
TCGA-GN-A26D TCGA-HR-A2OG TCGA-HR-A2OH TCGA-IH-A3EA 
         447           NA           NA          383 
Variable 1:'AGE':	nDistinctValues=67,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=88,	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=FALSE.
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"                                   
[2] "PRIMARY.SITE.OF.DISEASE"               
[3] "GENDER"                                
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[5] "DISTANT.METASTASIS"                    
[6] "LYMPH.NODE.METASTASIS"                 
[7] "TUMOR.STAGECODE"                       
[8] "NEOPLASM.DISEASESTAGE"                 
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 T0  T1 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 T4A T4B TIS  TX 
  6   4  14   3  18  17   6   4  24  14   6   8  49   1  12 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 202 columns, 1 survival variables, and 8 non-survival variables.
AGE, nv=67, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, 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    5  9
  1P GAIN WILD-TYPE 54 46
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               14               100 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                9                46 
$`1P GAIN MUTATED`
TCGA-D3-A2J8 TCGA-DA-A1IC TCGA-EB-A41A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L 
        8.38         6.64         0.26        11.15        38.63         1.08 
TCGA-EE-A2A2 TCGA-ER-A19F TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FS-A1ZN TCGA-GN-A266 
       23.90        11.11         6.58         5.95        24.00        10.09 
TCGA-GN-A26A TCGA-GN-A26C 
       12.16        24.00 

$`1P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
       10.26        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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2.86         3.88        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC 
        0.53         0.43         1.35         1.28         1.18         0.30 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X 
        0.13         0.53         0.10         0.20         0.39        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-A29H TCGA-EE-A29M 
        5.13         8.81         7.96        37.97         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-A2A5 TCGA-EE-A2A6 
        2.43         8.09        11.31        25.28         9.67         8.94 
TCGA-ER-A19D TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
        3.52         4.18        12.99        28.64        42.84        78.44 
TCGA-ER-A3PL TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
        1.71        12.10        10.09        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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       15.35        24.85        15.35        31.33        84.72        16.21 
TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26D TCGA-IH-A3EA 
       15.39         5.59        14.70        12.59 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.26              0.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            38.63             98.76 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            10.60             10.52 
[1] "0.3 - 38.6 (10.6)" "0.1 - 98.8 (10.5)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
  "1P GAIN MUTATED" "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-A263 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
  "1P GAIN MUTATED" "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-A263 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
  "1P GAIN MUTATED" "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-A263 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D1V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1P GAIN MUTATED                    3             3
  1P GAIN WILD-TYPE                 24            23
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1P GAIN MUTATED                                                                                          7
  1P GAIN WILD-TYPE                                                                                       30
                   vv
clus                REGIONAL LYMPH NODE
  1P GAIN MUTATED                    13
  1P GAIN WILD-TYPE                  99
D1V3, multiclass
                                                                                          clus
vv                                                                                         1P GAIN MUTATED
  DISTANT METASTASIS                                                                                     3
  PRIMARY TUMOR                                                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   13
                                                                                          clus
vv                                                                                         1P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      24
  PRIMARY TUMOR                                                                                           23
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                30
  REGIONAL LYMPH NODE                                                                                     99
D1V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      9   17
  1P GAIN WILD-TYPE   67  109
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               9                67
  MALE                17               109
D1V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   25
  1P GAIN WILD-TYPE    2  174
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                1                 2
  YES              25               174
                   vv
clus                 M0  M1 M1A M1B M1C
  1P GAIN MUTATED    25   0   0   0   0
  1P GAIN WILD-TYPE 151   2   2   2   3
D1V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  1P GAIN MUTATED   13  0   4   3  0   2   1   1  1  0
  1P GAIN WILD-TYPE 97  2   4  14  1   3  13   5 18  5
D1V7, multiclass
D1V8, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1P GAIN MUTATED             0       2        3        3        1         0
  1P GAIN WILD-TYPE           4      15        7       12       19         9
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1P GAIN MUTATED           0         3         0          4          5
  1P GAIN WILD-TYPE        10        20         9          3         16
                   vv
clus                STAGE IIIC STAGE IV
  1P GAIN MUTATED            3        0
  1P GAIN WILD-TYPE         24        7
D1V9, multiclass

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   19 18
  1Q GAIN WILD-TYPE 40 37
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               37                77 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               18                37 
$`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-D9-A3Z4 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
        2.86         3.88        39.19         9.99        44.52        36.69 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A41A TCGA-EE-A17Z TCGA-EE-A20B 
        4.93         6.64         7.00         0.26         6.31        36.07 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A1 
       11.15        38.63         1.08         8.84         9.99        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A3ET TCGA-ER-A3PL 
       23.90         8.94         3.52        11.11         6.58         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
        5.95        72.16        24.00        10.09        16.21        12.16 
TCGA-GN-A26D 
       14.70 

$`1Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       32.55        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J9 TCGA-D3-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-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A1NK 
       25.15        22.36        19.36        17.56        14.83         0.53 
TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF 
        0.43         1.35         1.28         1.18         0.30         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A181 
        0.53         0.10         0.20         0.39        11.57         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
        1.35        12.20         4.27         5.13         8.81         7.96 
TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       37.97         4.41        27.12         9.47        12.03         8.12 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-ER-A19J 
        6.48         2.43         8.09        11.31         9.67         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A2OS TCGA-FR-A3R1 
       12.99        28.64        42.84        78.44        12.10        10.09 
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-A263 TCGA-GN-A264 
        1.02         0.13        15.35        24.85        15.35        31.33 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26C TCGA-IH-A3EA 
       84.72        15.39         5.59        24.00        12.59 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.26              0.10 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            72.16             98.76 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             9.99             11.31 
[1] "0.3 - 72.2 (10.0)" "0.1 - 98.8 (11.3)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FS-A1ZN        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-A263 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FS-A1ZN        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-A263 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FS-A1ZN        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-A263 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1Q GAIN MUTATED                   13             4
  1Q GAIN WILD-TYPE                 14            22
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1Q GAIN MUTATED                                                                                         17
  1Q GAIN WILD-TYPE                                                                                       20
                   vv
clus                REGIONAL LYMPH NODE
  1Q GAIN MUTATED                    33
  1Q GAIN WILD-TYPE                  79
D2V3, multiclass
                                                                                          clus
vv                                                                                         1Q GAIN MUTATED
  DISTANT METASTASIS                                                                                    13
  PRIMARY TUMOR                                                                                          4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              17
  REGIONAL LYMPH NODE                                                                                   33
                                                                                          clus
vv                                                                                         1Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      14
  PRIMARY TUMOR                                                                                           22
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                20
  REGIONAL LYMPH NODE                                                                                     79
D2V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     25   42
  1Q GAIN WILD-TYPE   51   84
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              25                51
  MALE                42                84
D2V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      0   67
  1Q GAIN WILD-TYPE    3  132
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                0                 3
  YES              67               132
                   vv
clus                 M0  M1 M1A M1B M1C
  1Q GAIN MUTATED    60   0   1   0   1
  1Q GAIN WILD-TYPE 116   2   1   2   2
D2V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  1Q GAIN MUTATED   35  0   4   9  0   4   3   4  4  0
  1Q GAIN WILD-TYPE 75  2   4   8  1   1  11   2 15  5
D2V7, multiclass
D2V8, 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        9       14         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1Q GAIN MUTATED           4         6         3          5         12
  1Q GAIN WILD-TYPE         6        17         6          2          9
                   vv
clus                STAGE IIIC STAGE IV
  1Q GAIN MUTATED            7        2
  1Q GAIN WILD-TYPE         20        5
D2V9, multiclass

Clustering(3) Variable = 2p gain mutation analysis
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    5  9
  2P GAIN WILD-TYPE 54 46
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               14               100 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                9                46 
$`2P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3MV TCGA-EB-A41B 
       16.47        70.16        22.55        11.41         5.39         0.10 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29R TCGA-ER-A19N 
        8.81         7.96        11.15         1.08         8.84        42.84 
TCGA-FR-A3YN TCGA-GN-A26C 
        5.95        24.00 

$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW 
        9.30         4.01         2.86         3.88        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D 
        7.00        17.56        14.83         0.53         0.43         1.35 
TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A 
        1.28         1.18         0.30         0.13         0.53         0.26 
TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        0.20         0.39        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-FR-A2OS TCGA-FR-A3R1 
       28.64        78.44         6.58         1.71        12.10        10.09 
TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
       72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       15.35        31.33        84.72        10.09        16.21        15.39 
TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26D TCGA-IH-A3EA 
        5.59        12.16        14.70        12.59 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.10              0.13 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            70.16             98.76 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            9.995            10.520 
[1] "0.1 - 70.2 (10.0)" "0.1 - 98.8 (10.5)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"2P GAIN WILD-TYPE" "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-A263 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"2P GAIN WILD-TYPE" "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-A263 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"2P GAIN WILD-TYPE" "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-A263 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D3V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2P GAIN MUTATED                    3             2
  2P GAIN WILD-TYPE                 24            24
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2P GAIN MUTATED                                                                                          5
  2P GAIN WILD-TYPE                                                                                       32
                   vv
clus                REGIONAL LYMPH NODE
  2P GAIN MUTATED                     9
  2P GAIN WILD-TYPE                 103
D3V3, multiclass
                                                                                          clus
vv                                                                                         2P GAIN MUTATED
  DISTANT METASTASIS                                                                                     3
  PRIMARY TUMOR                                                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                    9
                                                                                          clus
vv                                                                                         2P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      24
  PRIMARY TUMOR                                                                                           24
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                32
  REGIONAL LYMPH NODE                                                                                    103
D3V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5   14
  2P GAIN WILD-TYPE   71  112
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               5                71
  MALE                14               112
D3V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1   18
  2P GAIN WILD-TYPE    2  181
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                1                 2
  YES              18               181
                   vv
clus                 M0  M1 M1A M1B M1C
  2P GAIN MUTATED    18   0   0   0   0
  2P GAIN WILD-TYPE 158   2   2   2   3
D3V6, multiclass
                   vv
clus                 N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  2P GAIN MUTATED     8   0   1   4   0   2   1   0   2   0
  2P GAIN WILD-TYPE 102   2   7  13   1   3  13   6  17   5
D3V7, multiclass
D3V8, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2P GAIN MUTATED             0       1        1        1        1         2
  2P GAIN WILD-TYPE           4      16        9       14       19         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  2P GAIN MUTATED           0         2         1          1          2
  2P GAIN WILD-TYPE        10        21         8          6         19
                   vv
clus                STAGE IIIC STAGE IV
  2P GAIN MUTATED            6        0
  2P GAIN WILD-TYPE         21        7
D3V9, multiclass

Clustering(4) Variable = 2q gain mutation analysis
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    5  8
  2Q GAIN WILD-TYPE 54 47
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13               101 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                8                47 
$`2Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3MV TCGA-EB-A3XF 
       16.47        70.16        22.55        11.41         5.39         0.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29L TCGA-EE-A29R TCGA-ER-A19N TCGA-FR-A3YN 
        8.81         7.96         1.08         8.84        42.84         5.95 
TCGA-GN-A26C 
       24.00 

$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW 
        9.30         4.01         2.86         3.88        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D 
        7.00        17.56        14.83         0.53         0.43         1.35 
TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B 
        1.28         1.18         0.30         0.53         0.26         0.10 
TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        0.20         0.39        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-FR-A2OS 
       12.99        28.64        78.44         6.58         1.71        12.10 
TCGA-FR-A3R1 TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 
       10.09        72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       24.85        15.35        31.33        84.72        10.09        16.21 
TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26D TCGA-IH-A3EA 
       15.39         5.59        12.16        14.70        12.59 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.13              0.10 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            70.16             98.76 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             8.84             10.78 
[1] "0.1 - 70.2 (8.8)"  "0.1 - 98.8 (10.8)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"2Q GAIN WILD-TYPE" "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-A263 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"2Q GAIN WILD-TYPE" "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-A263 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"2Q GAIN WILD-TYPE" "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-A263 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D4V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2Q GAIN MUTATED                    2             2
  2Q GAIN WILD-TYPE                 25            24
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2Q GAIN MUTATED                                                                                          5
  2Q GAIN WILD-TYPE                                                                                       32
                   vv
clus                REGIONAL LYMPH NODE
  2Q GAIN MUTATED                     8
  2Q GAIN WILD-TYPE                 104
D4V3, multiclass
                                                                                          clus
vv                                                                                         2Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                    8
                                                                                          clus
vv                                                                                         2Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      25
  PRIMARY TUMOR                                                                                           24
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                32
  REGIONAL LYMPH NODE                                                                                    104
D4V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4   13
  2Q GAIN WILD-TYPE   72  113
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               4                72
  MALE                13               113
D4V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1   16
  2Q GAIN WILD-TYPE    2  183
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                1                 2
  YES              16               183
                   vv
clus                 M0  M1 M1A M1B M1C
  2Q GAIN MUTATED    16   0   0   0   0
  2Q GAIN WILD-TYPE 160   2   2   2   3
D4V6, multiclass
                   vv
clus                 N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  2Q GAIN MUTATED     7   0   1   3   0   2   1   0   2   0
  2Q GAIN WILD-TYPE 103   2   7  14   1   3  13   6  17   5
D4V7, multiclass
D4V8, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2Q GAIN MUTATED             0       1        1        1        0         2
  2Q GAIN WILD-TYPE           4      16        9       14       20         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  2Q GAIN MUTATED           0         2         1          1          2
  2Q GAIN WILD-TYPE        10        21         8          6         19
                   vv
clus                STAGE IIIC STAGE IV
  2Q GAIN MUTATED            5        0
  2Q GAIN WILD-TYPE         22        7
D4V9, multiclass

Clustering(5) Variable = 3p gain mutation analysis
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    7  7
  3P GAIN WILD-TYPE 52 48
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               14               100 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                7                48 
$`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 TCGA-GN-A26C 
       10.09        24.00 

$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        3.88        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-A1IB 
       13.68         9.99        44.52        36.69        25.15        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D 
        6.64        19.36        14.83         0.53         0.43         1.35 
TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A 
        1.28         1.18         0.30         0.13         0.53         0.26 
TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        0.10         0.20         0.39        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-A29N TCGA-EE-A29P 
       37.97        11.15        38.63         4.41         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-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J 
       23.90         9.67         8.94         3.52        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3PL TCGA-FR-A2OS 
       12.99        28.64        42.84        78.44         1.71        12.10 
TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 
       10.09         5.95        72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       24.85        15.35        31.33        84.72        16.21        15.39 
TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26D TCGA-IH-A3EA 
        5.59        12.16        14.70        12.59 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             1.08              0.10 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            30.87             98.76 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            7.905            11.230 
[1] "1.1 - 30.9 (7.9)"  "0.1 - 98.8 (11.2)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D5V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3P GAIN MUTATED                    7             2
  3P GAIN WILD-TYPE                 20            24
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3P GAIN MUTATED                                                                                          5
  3P GAIN WILD-TYPE                                                                                       32
                   vv
clus                REGIONAL LYMPH NODE
  3P GAIN MUTATED                     6
  3P GAIN WILD-TYPE                 106
D5V3, multiclass
                                                                                          clus
vv                                                                                         3P GAIN MUTATED
  DISTANT METASTASIS                                                                                     7
  PRIMARY TUMOR                                                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                    6
                                                                                          clus
vv                                                                                         3P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      20
  PRIMARY TUMOR                                                                                           24
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                32
  REGIONAL LYMPH NODE                                                                                    106
D5V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     10   10
  3P GAIN WILD-TYPE   66  116
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              10                66
  MALE                10               116
D5V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1   19
  3P GAIN WILD-TYPE    2  180
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                1                 2
  YES              19               180
                   vv
clus                 M0  M1 M1A M1B M1C
  3P GAIN MUTATED    18   0   0   0   0
  3P GAIN WILD-TYPE 158   2   2   2   3
D5V6, multiclass
                   vv
clus                 N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  3P GAIN MUTATED     8   0   2   2   0   1   2   0   2   1
  3P GAIN WILD-TYPE 102   2   6  15   1   4  12   6  17   4
D5V7, multiclass
D5V8, 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       14       19         8
                   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        22         9          6         17
                   vv
clus                STAGE IIIC STAGE IV
  3P GAIN MUTATED            4        0
  3P GAIN WILD-TYPE         23        7
D5V9, multiclass

Clustering(6) Variable = 3q gain mutation analysis
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    8  9
  3Q GAIN WILD-TYPE 51 46
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               17                97 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                9                46 
$`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 TCGA-GN-A26C 
        6.58         3.22        10.09        12.16        24.00 

$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        3.88        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-A1IB 
       13.68         9.99        44.52        36.69        25.15        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D 
        6.64        19.36        14.83         0.53         0.43         1.35 
TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A 
        1.28         1.18         0.30         0.13         0.53         0.26 
TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        0.10         0.20         0.39        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
       12.20         4.27        36.07         7.96        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       38.63         4.41         1.08         9.47        12.03         8.12 
TCGA-EE-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-A19N TCGA-ER-A1A1 TCGA-ER-A3PL TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN 
       42.84        78.44         1.71        12.10        10.09         5.95 
TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
       72.16        24.00         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-A263 
        0.20         1.02         0.13        15.35        24.85        15.35 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26D 
       31.33        84.72        16.21        15.39         5.59        14.70 
TCGA-IH-A3EA 
       12.59 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             1.35              0.10 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            30.87             98.76 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             8.81             11.15 
[1] "1.4 - 30.9 (8.8)"  "0.1 - 98.8 (11.2)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"3Q GAIN WILD-TYPE" "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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"3Q GAIN WILD-TYPE" "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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D6V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3Q GAIN MUTATED                    8             2
  3Q GAIN WILD-TYPE                 19            24
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3Q GAIN MUTATED                                                                                          6
  3Q GAIN WILD-TYPE                                                                                       31
                   vv
clus                REGIONAL LYMPH NODE
  3Q GAIN MUTATED                     9
  3Q GAIN WILD-TYPE                 103
D6V3, multiclass
                                                                                          clus
vv                                                                                         3Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     8
  PRIMARY TUMOR                                                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               6
  REGIONAL LYMPH NODE                                                                                    9
                                                                                          clus
vv                                                                                         3Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      19
  PRIMARY TUMOR                                                                                           24
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                31
  REGIONAL LYMPH NODE                                                                                    103
D6V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     12   13
  3Q GAIN WILD-TYPE   64  113
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              12                64
  MALE                13               113
D6V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1   24
  3Q GAIN WILD-TYPE    2  175
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                1                 2
  YES              24               175
                   vv
clus                 M0  M1 M1A M1B M1C
  3Q GAIN MUTATED    23   0   0   0   0
  3Q GAIN WILD-TYPE 153   2   2   2   3
D6V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  3Q GAIN MUTATED   12  0   3   3  0   1   2   0  1  1
  3Q GAIN WILD-TYPE 98  2   5  14  1   4  12   6 18  4
D6V7, multiclass
D6V8, 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       13       17         8
                   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        22         9          5         17
                   vv
clus                STAGE IIIC STAGE IV
  3Q GAIN MUTATED            4        0
  3Q GAIN WILD-TYPE         23        7
D6V9, multiclass

Clustering(7) Variable = 4p gain mutation analysis
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    7  3
  4P GAIN WILD-TYPE 52 52
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10               104 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                52 
$`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-D9-A3Z4 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        2.86         3.88        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-A3F8 TCGA-EB-A1NK TCGA-EB-A24C 
        6.64        19.36         7.00        14.83         0.53         0.43 
TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 
        1.35         1.28         1.18         0.30         0.13         0.53 
TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z 
        0.26         0.10         0.20         0.39        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-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08        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-A3PL TCGA-FR-A2OS TCGA-FR-A3R1 
       28.64        42.84        78.44         1.71        12.10        10.09 
TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
       72.16        24.00         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-A263 
        0.20         1.02         0.13        15.35        24.85        15.35 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A 
       84.72        10.09        16.21        15.39         5.59        12.16 
TCGA-GN-A26C TCGA-IH-A3EA 
       24.00        12.59 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             3.22              0.10 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            48.79             98.76 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            14.01             10.09 
[1] "3.2 - 48.8 (14.0)" "0.1 - 98.8 (10.1)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
[1] "hr=" "2.1"
D7V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4P GAIN MUTATED                    3             0
  4P GAIN WILD-TYPE                 24            26
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4P GAIN MUTATED                                                                                          4
  4P GAIN WILD-TYPE                                                                                       33
                   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                                                                                      24
  PRIMARY TUMOR                                                                                           26
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                33
  REGIONAL LYMPH NODE                                                                                    102
D7V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      8    9
  4P GAIN WILD-TYPE   68  117
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               8                68
  MALE                 9               117
D7V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   17
  4P GAIN WILD-TYPE    3  182
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                0                 3
  YES              17               182
                   vv
clus                 M0  M1 M1A M1B M1C
  4P GAIN MUTATED    15   0   0   0   0
  4P GAIN WILD-TYPE 161   2   2   2   3
D7V6, 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 102   2   5  16   1   5  13   5  17   5
D7V7, multiclass
D7V8, 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       14       19         9
                   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        19         7          5         19
                   vv
clus                STAGE IIIC STAGE IV
  4P GAIN MUTATED            2        0
  4P GAIN WILD-TYPE         25        7
D7V9, multiclass

Clustering(8) Variable = 4q gain mutation analysis
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    6  3
  4Q GAIN WILD-TYPE 53 52
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                9               105 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                52 
$`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-D9-A3Z4 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        2.86         3.88        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-A3F8 TCGA-EB-A1NK TCGA-EB-A24C 
        6.64        19.36         7.00        14.83         0.53         0.43 
TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 
        1.35         1.28         1.18         0.30         0.13         0.53 
TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z 
        0.26         0.10         0.20         0.39        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-A29E TCGA-EE-A29H TCGA-EE-A29L 
        8.81         7.96        37.97        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-A3ET TCGA-ER-A3PL TCGA-FR-A2OS TCGA-FR-A3R1 
       42.84        78.44         6.58         1.71        12.10        10.09 
TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
       72.16        24.00         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-A263 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 
       15.35        84.72        10.09        16.21        15.39         5.59 
TCGA-GN-A26A TCGA-GN-A26C TCGA-IH-A3EA 
       12.16        24.00        12.59 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             5.95              0.10 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            48.79             98.76 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            14.70             10.03 
[1] "6.0 - 48.8 (14.7)" "0.1 - 98.8 (10.0)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
[1] "hr=" "2.2"
D8V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4Q GAIN MUTATED                    1             0
  4Q GAIN WILD-TYPE                 26            26
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4Q GAIN MUTATED                                                                                          2
  4Q GAIN WILD-TYPE                                                                                       35
                   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                                                                                      26
  PRIMARY TUMOR                                                                                           26
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                35
  REGIONAL LYMPH NODE                                                                                    102
D8V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5    8
  4Q GAIN WILD-TYPE   71  118
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               5                71
  MALE                 8               118
D8V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   13
  4Q GAIN WILD-TYPE    3  186
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                0                 3
  YES              13               186
                   vv
clus                 M0  M1 M1A M1B M1C
  4Q GAIN MUTATED    10   0   0   0   0
  4Q GAIN WILD-TYPE 166   2   2   2   3
D8V6, 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 106   2   6  15   1   5  13   6  17   5
D8V7, multiclass
D8V8, 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       14       20         9
                   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        20         8          6         19
                   vv
clus                STAGE IIIC STAGE IV
  4Q GAIN MUTATED            3        0
  4Q GAIN WILD-TYPE         24        7
D8V9, multiclass

Clustering(9) Variable = 5p gain mutation analysis
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    8  5
  5P GAIN WILD-TYPE 51 50
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               13               101 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                5                50 
$`5P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A2JF TCGA-D3-A2JK TCGA-DA-A1HV TCGA-EB-A1NK TCGA-EB-A3Y6 
       32.55        30.87         6.35        48.79         0.53         0.53 
TCGA-EB-A42Y TCGA-EE-A20H TCGA-EE-A29T TCGA-EE-A2A0 TCGA-ER-A19M TCGA-FW-A3I3 
        0.20         8.81         6.48        11.31        28.64         0.20 
TCGA-FW-A3TU 
        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-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE 
        8.38        21.14        11.41        15.25        45.70        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A3Z4 
       24.00         9.30         5.39         4.01         2.86         3.88 
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-EB-A24C TCGA-EB-A24D 
       19.36         7.00        17.56        14.83         0.43         1.35 
TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A41A TCGA-EB-A41B 
        1.28         1.18         0.30         0.13         0.26         0.10 
TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.39        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-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-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-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-A2OS 
       12.99        42.84        78.44         6.58         1.71        12.10 
TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 
       10.09         5.95        72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       15.35        31.33        84.72        10.09        16.21        15.39 
TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
        5.59        12.16        24.00        14.70        12.59 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.13              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            48.79             98.76 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             6.48             11.11 
[1] "0.1 - 48.8 (6.5)"  "0.1 - 98.8 (11.1)"
       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 MUTATED" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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 MUTATED" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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 MUTATED" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D9V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5P GAIN MUTATED                    6             4
  5P GAIN WILD-TYPE                 21            22
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5P GAIN MUTATED                                                                                          1
  5P GAIN WILD-TYPE                                                                                       36
                   vv
clus                REGIONAL LYMPH NODE
  5P GAIN MUTATED                    13
  5P GAIN WILD-TYPE                  99
D9V3, multiclass
                                                                                          clus
vv                                                                                         5P GAIN MUTATED
  DISTANT METASTASIS                                                                                     6
  PRIMARY TUMOR                                                                                          4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                   13
                                                                                          clus
vv                                                                                         5P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      21
  PRIMARY TUMOR                                                                                           22
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                36
  REGIONAL LYMPH NODE                                                                                     99
D9V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11   13
  5P GAIN WILD-TYPE   65  113
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              11                65
  MALE                13               113
D9V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      0   24
  5P GAIN WILD-TYPE    3  175
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                0                 3
  YES              24               175
                   vv
clus                 M0  M1 M1A M1B M1C
  5P GAIN MUTATED    21   1   0   1   0
  5P GAIN WILD-TYPE 155   1   2   1   3
D9V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  5P GAIN MUTATED   17  0   0   1  0   1   2   0  1  1
  5P GAIN WILD-TYPE 93  2   8  16  1   4  12   6 18  4
D9V7, multiclass
D9V8, 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         2
  5P GAIN WILD-TYPE           3      14        8       14       18         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5P GAIN MUTATED           0         5         0          0          2
  5P GAIN WILD-TYPE        10        18         9          7         19
                   vv
clus                STAGE IIIC STAGE IV
  5P GAIN MUTATED            1        1
  5P GAIN WILD-TYPE         26        6
D9V9, multiclass

Clustering(10) Variable = 5q gain mutation analysis
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    2  0
  5Q GAIN WILD-TYPE 57 55
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2               112 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                0                55 
$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2.86         3.88        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
       14.83         0.53         0.43         1.35         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y 
        0.30         0.13         0.53         0.26         0.10         0.20 
TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.39        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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN 
       78.44         6.58         1.71        12.10        10.09         5.95 
TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
       72.16        24.00         8.81        53.82         3.22        10.78 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A263 
        6.41         0.20         1.02        15.35        24.85        15.35 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 
       31.33        84.72        10.09        16.21        15.39         5.59 
TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       12.16        24.00        14.70        12.59 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.13              0.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            30.87             98.76 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            15.50             10.52 
[1] "0.1 - 30.9 (15.5)" "0.1 - 98.8 (10.5)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2               112 
       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-D9-A3Z4 
"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-EB-A1NK        TCGA-EB-A24C        TCGA-EB-A24D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC        TCGA-EB-A3XF 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B        TCGA-EB-A42Y 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EB-A42Z        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-A2OS 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A        TCGA-FS-A1ZN 
"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-A263        TCGA-GN-A264        TCGA-GN-A265 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A269 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26C        TCGA-GN-A26D        TCGA-IH-A3EA 
"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                 24            26
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5Q GAIN MUTATED                                                                                          0
  5Q GAIN WILD-TYPE                                                                                       37
                   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                                                                                      24
  PRIMARY TUMOR                                                                                           26
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                37
  REGIONAL LYMPH NODE                                                                                    108
D10V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    5
  5Q GAIN WILD-TYPE   74  121
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               2                74
  MALE                 5               121
D10V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    7
  5Q GAIN WILD-TYPE    3  192
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                0                 3
  YES               7               192
                   vv
clus                 M0  M1 M1A M1B M1C
  5Q GAIN MUTATED     6   0   0   0   0
  5Q GAIN WILD-TYPE 170   2   2   2   3
D10V6, 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 105   2   8  17   1   4  14   6  19   5
D10V7, multiclass
D10V8, 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       15       18         8
                   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        23         9          7         21
                   vv
clus                STAGE IIIC STAGE IV
  5Q GAIN MUTATED            0        0
  5Q GAIN WILD-TYPE         27        7
D10V9, multiclass

Clustering(11) Variable = 6p gain mutation analysis
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   14 22
  6P GAIN WILD-TYPE 45 33
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               36                78 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               22                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-EB-A3XF TCGA-EB-A41A 
       10.03        13.68         4.93         7.00         0.13         0.26 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A29P TCGA-EE-A29R 
        6.31         1.12         4.27         8.81        12.03         8.84 
TCGA-EE-A29S TCGA-EE-A2A5 TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-FR-A2OS 
        9.99         9.67         4.18        28.64        42.84        12.10 
TCGA-FR-A3R1 TCGA-FS-A1ZN TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 
       10.09        24.00         3.22         0.20         0.13        31.33 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26D TCGA-IH-A3EA 
       10.09        16.21         5.59        12.16        14.70        12.59 

$`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-D9-A3Z4 TCGA-DA-A1HW TCGA-DA-A1HY 
        5.39         4.01         2.86         3.88        35.80        51.12 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
       39.19         9.99        44.52        36.69        25.15        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A1NK TCGA-EB-A24C 
        6.64        19.36        17.56        14.83         0.53         0.43 
TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3Y6 TCGA-EB-A41B 
        1.35         1.28         1.18         0.30         0.53         0.10 
TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B 
        0.20         0.39        11.57         1.35        12.20        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-A29Q TCGA-EE-A29T TCGA-EE-A29V 
        1.08        27.12         9.47         8.12         6.48         2.43 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19D 
        8.09        11.31        25.28        23.90         8.94         3.52 
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
       11.11        12.99        78.44         6.58         1.71         5.95 
TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 
       72.16         8.81        53.82        10.78         6.41         1.02 
TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A263 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26C 
       15.35        24.85        15.35        84.72        15.39        24.00 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.13              0.10 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            98.76             84.72 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           10.090            10.945 
[1] "0.1 - 98.8 (10.1)" "0.1 - 84.7 (10.9)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
  "6P GAIN MUTATED" "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-A263 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
  "6P GAIN MUTATED" "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-A263 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
  "6P GAIN MUTATED" "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-A263 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" 
[1] "hr=" "1.6"
D11V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6P GAIN MUTATED                   14             7
  6P GAIN WILD-TYPE                 13            19
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6P GAIN MUTATED                                                                                         10
  6P GAIN WILD-TYPE                                                                                       27
                   vv
clus                REGIONAL LYMPH NODE
  6P GAIN MUTATED                    36
  6P GAIN WILD-TYPE                  76
D11V3, multiclass
                                                                                          clus
vv                                                                                         6P GAIN MUTATED
  DISTANT METASTASIS                                                                                    14
  PRIMARY TUMOR                                                                                          7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              10
  REGIONAL LYMPH NODE                                                                                   36
                                                                                          clus
vv                                                                                         6P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      13
  PRIMARY TUMOR                                                                                           19
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                27
  REGIONAL LYMPH NODE                                                                                     76
D11V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     28   39
  6P GAIN WILD-TYPE   48   87
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              28                48
  MALE                39                87
D11V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0   67
  6P GAIN WILD-TYPE    3  132
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                0                 3
  YES              67               132
                   vv
clus                 M0  M1 M1A M1B M1C
  6P GAIN MUTATED    56   2   1   0   0
  6P GAIN WILD-TYPE 120   0   1   2   3
D11V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  6P GAIN MUTATED   40  0   5   4  0   2   3   0  6  0
  6P GAIN WILD-TYPE 70  2   3  13  1   3  11   6 13  5
D11V7, multiclass
D11V8, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6P GAIN MUTATED             1       5        3        5        6         3
  6P GAIN WILD-TYPE           3      12        7       10       14         6
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6P GAIN MUTATED           5        11         0          5          5
  6P GAIN WILD-TYPE         5        12         9          2         16
                   vv
clus                STAGE IIIC STAGE IV
  6P GAIN MUTATED            7        2
  6P GAIN WILD-TYPE         20        5
D11V9, multiclass

Clustering(12) Variable = 6q gain mutation analysis
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    5  5
  6Q GAIN WILD-TYPE 54 50
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               10               104 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5                50 
$`6Q GAIN MUTATED`
TCGA-D3-A1Q7 TCGA-DA-A1I0 TCGA-EB-A3XF TCGA-EE-A29R TCGA-ER-A19M TCGA-FS-A1ZN 
       98.76        10.03         0.13         8.84        28.64        24.00 
TCGA-FS-A4F2 TCGA-FW-A3TU TCGA-GN-A269 TCGA-IH-A3EA 
        3.22         0.13         5.59        12.59 

$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
        2.86         3.88        48.79        35.80        51.12        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC 
        0.53         0.43         1.35         1.28         1.18         0.30 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X 
        0.53         0.26         0.10         0.20         0.39        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-A2OS 
       12.99        42.84        78.44         6.58         1.71        12.10 
TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 
       10.09         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-A263 
        6.41         0.20         1.02        15.35        24.85        15.35 
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-A26C TCGA-GN-A26D 
       24.00        14.70 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.13              0.10 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            98.76             84.72 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            9.435            10.945 
[1] "0.1 - 98.8 (9.4)"  "0.1 - 84.7 (10.9)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
  "6Q GAIN MUTATED" "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-A263 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
  "6Q GAIN MUTATED" "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-A263 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
  "6Q GAIN MUTATED" "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-A263 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
[1] "hr=" "1.1"
D12V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6Q GAIN MUTATED                    3             4
  6Q GAIN WILD-TYPE                 24            22
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6Q GAIN MUTATED                                                                                          2
  6Q GAIN WILD-TYPE                                                                                       35
                   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                                                                                          4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    7
                                                                                          clus
vv                                                                                         6Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      24
  PRIMARY TUMOR                                                                                           22
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                35
  REGIONAL LYMPH NODE                                                                                    105
D12V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      6   10
  6Q GAIN WILD-TYPE   70  116
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               6                70
  MALE                10               116
D12V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   16
  6Q GAIN WILD-TYPE    3  183
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                0                 3
  YES              16               183
                   vv
clus                 M0  M1 M1A M1B M1C
  6Q GAIN MUTATED    14   0   1   0   0
  6Q GAIN WILD-TYPE 162   2   1   2   3
D12V6, multiclass
                   vv
clus                 N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  6Q GAIN MUTATED    10   0   1   2   0   0   0   0   2   0
  6Q GAIN WILD-TYPE 100   2   7  15   1   5  14   6  17   5
D12V7, multiclass
D12V8, 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       12       18         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6Q GAIN MUTATED           1         3         0          1          0
  6Q GAIN WILD-TYPE         9        20         9          6         21
                   vv
clus                STAGE IIIC STAGE IV
  6Q GAIN MUTATED            3        0
  6Q GAIN WILD-TYPE         24        7
D12V9, multiclass

Clustering(13) Variable = 7p gain mutation analysis
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   21 27
  7P GAIN WILD-TYPE 38 28
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               48                66 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               27                28 
$`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-EB-A1NK 
       44.52        36.69        25.15         4.93         6.64         0.53 
TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XC TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A181 
        1.35         1.28         0.30         0.20         0.39         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-A3R1 TCGA-FR-A3YN TCGA-FS-A1ZR TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-GN-A264 
       10.09         5.95         8.81         3.22         0.20        31.33 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D 
       10.09        16.21         5.59        12.16        24.00        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-D9-A3Z4 TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 
        4.01         3.88        35.80        39.19        22.36        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A24C TCGA-EB-A3XB TCGA-EB-A3XF 
        7.00        17.56        14.83         0.43         1.18         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 
        0.53         0.26         0.10        11.57         6.31         1.35 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29L 
       12.20         4.27        36.07         5.13         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       27.12         8.12         8.84         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L 
       25.28        23.90         9.67         3.52        11.11        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A2OS TCGA-FR-A44A 
       28.64        42.84        78.44         6.58        12.10        72.16 
TCGA-FS-A1ZN TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
       24.00        53.82        10.78         6.41         1.02         0.13 
TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A263 TCGA-GN-A265 TCGA-GN-A268 TCGA-IH-A3EA 
       15.35        24.85        15.35        84.72        15.39        12.59 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              0.2               0.1 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            70.16             98.76 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           10.010            11.835 
[1] "0.2 - 70.2 (10.0)" "0.1 - 98.8 (11.8)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D13V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7P GAIN MUTATED                   10            11
  7P GAIN WILD-TYPE                 17            15
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7P GAIN MUTATED                                                                                         20
  7P GAIN WILD-TYPE                                                                                       17
                   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                                                                                         11
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              20
  REGIONAL LYMPH NODE                                                                                   44
                                                                                          clus
vv                                                                                         7P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      17
  PRIMARY TUMOR                                                                                           15
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                17
  REGIONAL LYMPH NODE                                                                                     68
D13V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     26   59
  7P GAIN WILD-TYPE   50   67
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              26                50
  MALE                59                67
D13V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      1   84
  7P GAIN WILD-TYPE    2  115
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                1                 2
  YES              84               115
                   vv
clus                 M0  M1 M1A M1B M1C
  7P GAIN MUTATED    73   2   2   0   2
  7P GAIN WILD-TYPE 103   0   0   2   1
D13V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  7P GAIN MUTATED   44  0   5  10  0   3   6   4  6  2
  7P GAIN WILD-TYPE 66  2   3   7  1   2   8   2 13  3
D13V7, multiclass
D13V8, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  7P GAIN MUTATED             2       6        5        3        8         3
  7P GAIN WILD-TYPE           2      11        5       12       12         6
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  7P GAIN MUTATED           2        11         3          5         12
  7P GAIN WILD-TYPE         8        12         6          2          9
                   vv
clus                STAGE IIIC STAGE IV
  7P GAIN MUTATED           11        5
  7P GAIN WILD-TYPE         16        2
D13V9, multiclass

Clustering(14) Variable = 7q gain mutation analysis
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   24 26
  7Q GAIN WILD-TYPE 35 29
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               50                64 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               26                29 
$`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-EB-A1NK TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XC 
       17.56        14.83         0.53         1.35         1.28         0.30 
TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29A 
        0.20         0.39         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-A3R1 TCGA-FR-A3YN TCGA-FS-A1ZR 
        8.94         4.18         1.71        10.09         5.95         8.81 
TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A269 TCGA-GN-A26A 
        3.22         0.20        31.33        16.21         5.59        12.16 
TCGA-GN-A26C TCGA-GN-A26D 
       24.00        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-D9-A3Z4 TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
        3.88        35.80        39.19        22.36        19.36         7.00 
TCGA-EB-A24C TCGA-EB-A3XB TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B 
        0.43         1.18         0.13         0.53         0.26         0.10 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
       11.57         6.31         1.35         4.27        36.07         5.13 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R 
       11.15         4.41         1.08        27.12         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        9.99         2.43         8.09        25.28        23.90         9.67 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
        3.52        11.11        12.99        28.64        42.84        78.44 
TCGA-ER-A3ET TCGA-FR-A2OS TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A4F0 TCGA-FS-A4F9 
        6.58        12.10        72.16        24.00        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A263 
        6.41         1.02         0.13        15.35        24.85        15.35 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-IH-A3EA 
       84.72        10.09        15.39        12.59 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              0.2               0.1 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            70.16             98.76 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            10.01             11.13 
[1] "0.2 - 70.2 (10.0)" "0.1 - 98.8 (11.1)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D14V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7Q GAIN MUTATED                   12            11
  7Q GAIN WILD-TYPE                 15            15
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7Q GAIN MUTATED                                                                                         19
  7Q GAIN WILD-TYPE                                                                                       18
                   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                                                                                         11
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              19
  REGIONAL LYMPH NODE                                                                                   44
                                                                                          clus
vv                                                                                         7Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      15
  PRIMARY TUMOR                                                                                           15
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                18
  REGIONAL LYMPH NODE                                                                                     68
D14V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     29   57
  7Q GAIN WILD-TYPE   47   69
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              29                47
  MALE                57                69
D14V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      1   85
  7Q GAIN WILD-TYPE    2  114
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                1                 2
  YES              85               114
                   vv
clus                 M0  M1 M1A M1B M1C
  7Q GAIN MUTATED    76   2   2   0   2
  7Q GAIN WILD-TYPE 100   0   0   2   1
D14V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  7Q GAIN MUTATED   45  0   5   9  0   4   7   4  7  2
  7Q GAIN WILD-TYPE 65  2   3   8  1   1   7   2 12  3
D14V7, multiclass
D14V8, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  7Q GAIN MUTATED             3       6        4        3        9         2
  7Q GAIN WILD-TYPE           1      11        6       12       11         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  7Q GAIN MUTATED           2        12         3          5         14
  7Q GAIN WILD-TYPE         8        11         6          2          7
                   vv
clus                STAGE IIIC STAGE IV
  7Q GAIN MUTATED           11        5
  7Q GAIN WILD-TYPE         16        2
D14V9, multiclass

Clustering(15) Variable = 8p gain mutation analysis
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   12 13
  8P GAIN WILD-TYPE 47 42
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               25                89 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               13                42 
$`8P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MV TCGA-D9-A3Z4 
       70.16        30.87        45.70        13.32         5.39         3.88 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-EB-A24D 
       51.12        39.19        13.68         9.99        17.56         1.35 
TCGA-EE-A181 TCGA-EE-A29R TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        1.12         8.84         4.18        12.99        28.64        42.84 
TCGA-FS-A1ZR TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26C 
        8.81         3.22         0.20        16.21        12.16        24.00 
TCGA-GN-A26D 
       14.70 

$`8P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        32.55        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF 
        8.38        21.14        11.41         6.35        15.25        24.00 
TCGA-D3-A3MO TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
        9.30         4.01         2.86        48.79        35.80        10.03 
TCGA-DA-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-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV 
       19.36         7.00        14.83         0.53         0.43         1.28 
TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B 
        1.18         0.30         0.13         0.53         0.26         0.10 
TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
        0.20         0.39        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-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-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-A2OS TCGA-FR-A3R1 
       11.11        78.44         6.58         1.71        12.10        10.09 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
        5.95        72.16        24.00        53.82        10.78         6.41 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A263 TCGA-GN-A264 
        1.02         0.13        15.35        24.85        15.35        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A269 TCGA-IH-A3EA 
       84.72        10.09        15.39         5.59        12.59 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              0.2               0.1 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            70.16             98.76 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            13.32             10.09 
[1] "0.2 - 70.2 (13.3)" "0.1 - 98.8 (10.1)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D15V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8P GAIN MUTATED                    6             3
  8P GAIN WILD-TYPE                 21            23
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8P GAIN MUTATED                                                                                         12
  8P GAIN WILD-TYPE                                                                                       25
                   vv
clus                REGIONAL LYMPH NODE
  8P GAIN MUTATED                    18
  8P GAIN WILD-TYPE                  94
D15V3, multiclass
                                                                                          clus
vv                                                                                         8P GAIN MUTATED
  DISTANT METASTASIS                                                                                     6
  PRIMARY TUMOR                                                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              12
  REGIONAL LYMPH NODE                                                                                   18
                                                                                          clus
vv                                                                                         8P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      21
  PRIMARY TUMOR                                                                                           23
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                25
  REGIONAL LYMPH NODE                                                                                     94
D15V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     12   27
  8P GAIN WILD-TYPE   64   99
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              12                64
  MALE                27                99
D15V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   38
  8P GAIN WILD-TYPE    2  161
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                1                 2
  YES              38               161
                   vv
clus                 M0  M1 M1A M1B M1C
  8P GAIN MUTATED    33   2   0   0   0
  8P GAIN WILD-TYPE 143   0   2   2   3
D15V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  8P GAIN MUTATED   18  0   3   4  0   2   4   0  5  0
  8P GAIN WILD-TYPE 92  2   5  13  1   3  10   6 14  5
D15V7, multiclass
D15V8, 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       13       15         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8P GAIN MUTATED           1         5         2          2          5
  8P GAIN WILD-TYPE         9        18         7          5         16
                   vv
clus                STAGE IIIC STAGE IV
  8P GAIN MUTATED            8        2
  8P GAIN WILD-TYPE         19        5
D15V9, multiclass

Clustering(16) Variable = 8q gain mutation analysis
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   19 21
  8Q GAIN WILD-TYPE 40 34
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               40                74 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               21                34 
$`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-D9-A3Z4 TCGA-DA-A1HY TCGA-DA-A1I0 
       13.32         9.30         5.39         3.88        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EB-A1NK 
       39.19        13.68         9.99         7.00        17.56         0.53 
TCGA-EB-A24D TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A42Y TCGA-EE-A17Z TCGA-EE-A181 
        1.35         0.13         0.53         0.20         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-FR-A2OS TCGA-FS-A1ZR TCGA-FS-A4F2 
       28.64        42.84         6.58        12.10         8.81         3.22 
TCGA-FW-A3I3 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        0.20        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-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XB 
        6.64        19.36        14.83         0.43         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A182 
        0.30         0.26         0.10         0.39        11.57         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-A29V TCGA-EE-A29X TCGA-EE-A2A0 
       12.03         8.12         9.99         2.43         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A1A1 
       25.28        23.90         8.94         3.52        11.11        78.44 
TCGA-ER-A3PL TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A4F0 
        1.71        10.09         5.95        72.16        24.00        53.82 
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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A269 
       15.35        31.33        84.72        10.09        15.39         5.59 
TCGA-GN-A26C TCGA-IH-A3EA 
       24.00        12.59 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.13              0.10 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            70.16             98.76 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            10.01             11.13 
[1] "0.1 - 70.2 (10.0)" "0.1 - 98.8 (11.1)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D16V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8Q GAIN MUTATED                    9             7
  8Q GAIN WILD-TYPE                 18            19
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8Q GAIN MUTATED                                                                                         16
  8Q GAIN WILD-TYPE                                                                                       21
                   vv
clus                REGIONAL LYMPH NODE
  8Q GAIN MUTATED                    31
  8Q GAIN WILD-TYPE                  81
D16V3, multiclass
                                                                                          clus
vv                                                                                         8Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     9
  PRIMARY TUMOR                                                                                          7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              16
  REGIONAL LYMPH NODE                                                                                   31
                                                                                          clus
vv                                                                                         8Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      18
  PRIMARY TUMOR                                                                                           19
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                21
  REGIONAL LYMPH NODE                                                                                     81
D16V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     22   41
  8Q GAIN WILD-TYPE   54   85
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              22                54
  MALE                41                85
D16V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      0   63
  8Q GAIN WILD-TYPE    3  136
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                0                 3
  YES              63               136
                   vv
clus                 M0  M1 M1A M1B M1C
  8Q GAIN MUTATED    55   2   1   0   0
  8Q GAIN WILD-TYPE 121   0   1   2   3
D16V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  8Q GAIN MUTATED   33  0   4   5  0   4   4   1  7  1
  8Q GAIN WILD-TYPE 77  2   4  12  1   1  10   5 12  4
D16V7, multiclass
D16V8, 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       11       14         6
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8Q GAIN MUTATED           3        11         3          3          8
  8Q GAIN WILD-TYPE         7        12         6          4         13
                   vv
clus                STAGE IIIC STAGE IV
  8Q GAIN MUTATED            9        2
  8Q GAIN WILD-TYPE         18        5
D16V9, multiclass

Clustering(17) Variable = 9p gain mutation analysis
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    1  1
  9P GAIN WILD-TYPE 58 54
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2               112 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                54 
$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2.86         3.88        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
       14.83         0.53         0.43         1.35         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y 
        0.30         0.13         0.53         0.26         0.10         0.20 
TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.39        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-A3PL TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A 
       78.44         1.71        12.10        10.09         5.95        72.16 
TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC 
       24.00         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-A263 
        0.20         1.02         0.13        15.35        24.85        15.35 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 
       31.33        84.72        10.09        16.21        15.39         5.59 
TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       12.16        24.00        14.70        12.59 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             6.58              0.10 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            22.55             98.76 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           14.565            10.520 
[1] "6.6 - 22.6 (14.6)" "0.1 - 98.8 (10.5)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2               112 
       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-D9-A3Z4 
"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-EB-A1NK        TCGA-EB-A24C        TCGA-EB-A24D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC        TCGA-EB-A3XF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B        TCGA-EB-A42Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EB-A42Z        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-A3PL        TCGA-FR-A2OS        TCGA-FR-A3R1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FR-A3YN        TCGA-FR-A44A        TCGA-FS-A1ZN        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-A263        TCGA-GN-A264        TCGA-GN-A265 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A269 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26C        TCGA-GN-A26D        TCGA-IH-A3EA 
"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                 27            26
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9P GAIN MUTATED                                                                                          1
  9P GAIN WILD-TYPE                                                                                       36
                   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                                                                                      27
  PRIMARY TUMOR                                                                                           26
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                36
  REGIONAL LYMPH NODE                                                                                    110
D17V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    1
  9P GAIN WILD-TYPE   74  125
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               2                74
  MALE                 1               125
D17V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0    3
  9P GAIN WILD-TYPE    3  196
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                0                 3
  YES               3               196
                   vv
clus                 M0  M1 M1A M1B M1C
  9P GAIN MUTATED     3   0   0   0   0
  9P GAIN WILD-TYPE 173   2   2   2   3
D17V6, 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 109   2   7  17   1   4  14   6  19   5
D17V7, multiclass
D17V8, 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       15       20         9
                   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        23         9          6         20
                   vv
clus                STAGE IIIC STAGE IV
  9P GAIN MUTATED            0        0
  9P GAIN WILD-TYPE         27        7
D17V9, multiclass

Clustering(18) Variable = 9q gain mutation analysis
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    2  1
  9Q GAIN WILD-TYPE 57 54
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3               111 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                54 
$`9Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-EB-A24D TCGA-FR-A44A 
       22.55         1.35        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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2.86         3.88        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC 
       14.83         0.53         0.43         1.28         1.18         0.30 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z 
        0.13         0.53         0.26         0.10         0.20         0.39 
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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FS-A1ZN 
        6.58         1.71        12.10        10.09         5.95        24.00 
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-A263 TCGA-GN-A264 
        1.02         0.13        15.35        24.85        15.35        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A 
       84.72        10.09        16.21        15.39         5.59        12.16 
TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       24.00        14.70        12.59 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.35              0.10 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            72.16             98.76 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            22.55             10.26 
[1] "1.4 - 72.2 (22.6)" "0.1 - 98.8 (10.3)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"9Q GAIN WILD-TYPE" "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-A263 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"9Q GAIN WILD-TYPE" "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-A263 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-FS-A1ZN        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"9Q GAIN WILD-TYPE" "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-A263 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
[1] "hr=" "2.3"
D18V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9Q GAIN MUTATED                    0             1
  9Q GAIN WILD-TYPE                 27            25
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9Q GAIN MUTATED                                                                                          0
  9Q GAIN WILD-TYPE                                                                                       37
                   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                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         9Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      27
  PRIMARY TUMOR                                                                                           25
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                37
  REGIONAL LYMPH NODE                                                                                    109
D18V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    2
  9Q GAIN WILD-TYPE   74  124
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               2                74
  MALE                 2               124
D18V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    4
  9Q GAIN WILD-TYPE    3  195
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                0                 3
  YES               4               195
                   vv
clus                 M0  M1 M1A M1B M1C
  9Q GAIN MUTATED     4   0   0   0   0
  9Q GAIN WILD-TYPE 172   2   2   2   3
D18V6, multiclass
                   vv
clus                 N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  9Q GAIN MUTATED     2   0   0   0   0   1   1   0   0   0
  9Q GAIN WILD-TYPE 108   2   8  17   1   4  13   6  19   5
D18V7, multiclass
D18V8, 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       15       19         9
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  9Q GAIN MUTATED           0         0         0          0          2
  9Q GAIN WILD-TYPE        10        23         9          7         19
                   vv
clus                STAGE IIIC STAGE IV
  9Q GAIN MUTATED            0        0
  9Q GAIN WILD-TYPE         27        7
D18V9, multiclass

Clustering(19) Variable = 11p gain mutation analysis
D19V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    4  4
  11P GAIN WILD-TYPE 55 51
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                106 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 51 
$`11P GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A3CE TCGA-DA-A3F3 TCGA-EE-A29T TCGA-ER-A19N TCGA-FR-A3R1 
       30.87        13.32         7.00         6.48        42.84        10.09 
TCGA-FS-A4F2 TCGA-GN-A26C 
        3.22        24.00 

$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        3.88        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-A3F5 TCGA-DA-A3F8 TCGA-EB-A1NK 
       22.36         6.64        19.36        17.56        14.83         0.53 
TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF 
        0.43         1.35         1.28         1.18         0.30         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X 
        0.53         0.26         0.10         0.20         0.39        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-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         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-A19L TCGA-ER-A19M TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A2OS 
       12.99        28.64        78.44         6.58         1.71        12.10 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 
        5.95        72.16        24.00         8.81        53.82        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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       15.35        31.33        84.72        10.09        16.21        15.39 
TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26D TCGA-IH-A3EA 
        5.59        12.16        14.70        12.59 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              3.22               0.10 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             42.84              98.76 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            11.705             10.520 
[1] "3.2 - 42.8 (11.7)" "0.1 - 98.8 (10.5)"
        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-D9-A3Z4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11P GAIN MUTATED                    2             2
  11P GAIN WILD-TYPE                 25            24
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11P GAIN MUTATED                                                                                          1
  11P GAIN WILD-TYPE                                                                                       36
                    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                                                                                           2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     8
                                                                                          clus
vv                                                                                         11P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       25
  PRIMARY TUMOR                                                                                            24
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 36
  REGIONAL LYMPH NODE                                                                                     104
D19V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3   10
  11P GAIN WILD-TYPE   73  116
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                3                 73
  MALE                 10                116
D19V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   12
  11P GAIN WILD-TYPE    2  187
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 1                  2
  YES               12                187
                    vv
clus                  M0  M1 M1A M1B M1C
  11P GAIN MUTATED    12   0   0   0   0
  11P GAIN WILD-TYPE 164   2   2   2   3
D19V6, multiclass
                    vv
clus                  N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  11P GAIN MUTATED     6   0   2   1   0   0   2   0   0   1
  11P GAIN WILD-TYPE 104   2   6  16   1   5  12   6  19   4
D19V7, multiclass
D19V8, 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       15       19         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11P GAIN MUTATED           0         2         1          1          2
  11P GAIN WILD-TYPE        10        21         8          6         19
                    vv
clus                 STAGE IIIC STAGE IV
  11P GAIN MUTATED            1        0
  11P GAIN WILD-TYPE         26        7
D19V9, multiclass

Clustering(20) Variable = 11q gain mutation analysis
D20V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    3  3
  11Q GAIN WILD-TYPE 56 52
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                108 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 52 
$`11Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A3CE TCGA-DA-A3F3 TCGA-EB-A42Y TCGA-ER-A19N TCGA-FS-A4F2 
       30.87        13.32         7.00         0.20        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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        3.88        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-A3F5 TCGA-DA-A3F8 TCGA-EB-A1NK 
       22.36         6.64        19.36        17.56        14.83         0.53 
TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF 
        0.43         1.35         1.28         1.18         0.30         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z 
        0.53         0.26         0.10         0.39        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-A2OS 
       12.99        28.64        78.44         6.58         1.71        12.10 
TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 
       10.09         5.95        72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       24.85        15.35        31.33        84.72        10.09        16.21 
TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       15.39         5.59        12.16        24.00        14.70        12.59 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               0.2                0.1 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             42.84              98.76 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             10.16              10.52 
[1] "0.2 - 42.8 (10.2)" "0.1 - 98.8 (10.5)"
        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-D9-A3Z4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D20V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11Q GAIN MUTATED                    2             1
  11Q GAIN WILD-TYPE                 25            25
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11Q GAIN MUTATED                                                                                          1
  11Q GAIN WILD-TYPE                                                                                       36
                    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                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         11Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       25
  PRIMARY TUMOR                                                                                            25
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 36
  REGIONAL LYMPH NODE                                                                                     107
D20V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    6
  11Q GAIN WILD-TYPE   73  120
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                 73
  MALE                  6                120
D20V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    9
  11Q GAIN WILD-TYPE    3  190
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 0                  3
  YES                9                190
                    vv
clus                  M0  M1 M1A M1B M1C
  11Q GAIN MUTATED     8   0   0   0   0
  11Q GAIN WILD-TYPE 168   2   2   2   3
D20V6, multiclass
                    vv
clus                  N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  11Q GAIN MUTATED     5   0   1   1   0   0   1   0   0   0
  11Q GAIN WILD-TYPE 105   2   7  16   1   5  13   6  19   5
D20V7, multiclass
D20V8, 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       15       19         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11Q GAIN MUTATED           0         2         1          0          2
  11Q GAIN WILD-TYPE        10        21         8          7         19
                    vv
clus                 STAGE IIIC STAGE IV
  11Q GAIN MUTATED            0        0
  11Q GAIN WILD-TYPE         27        7
D20V9, multiclass

Clustering(21) Variable = 12p gain mutation analysis
D21V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    5 10
  12P GAIN WILD-TYPE 54 45
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                15                 99 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                10                 45 
$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW 
        9.30         4.01         2.86         3.88        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       25.15        22.36         6.64        19.36         7.00        14.83 
TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC 
        0.53         0.43         1.35         1.28         1.18         0.30 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z 
        0.13         0.53         0.26         0.10         0.20         0.39 
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-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-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.47        12.03         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-A19N 
       25.28        23.90         9.67         3.52        11.11        42.84 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A 
       78.44         6.58        12.10        10.09         5.95        72.16 
TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC 
       24.00         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-A263 
        0.20         1.02         0.13        15.35        24.85        15.35 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 
       31.33        84.72        10.09        16.21        15.39         5.59 
TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       24.00        14.70        12.59 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.71               0.10 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             70.16              98.76 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             12.99              10.09 
[1] "1.7 - 70.2 (13.0)" "0.1 - 98.8 (10.1)"
        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-D9-A3Z4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "12P GAIN MUTATED"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "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-D9-A3Z4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "12P GAIN MUTATED"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "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-D9-A3Z4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "12P GAIN MUTATED"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "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                 24            26
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12P GAIN MUTATED                                                                                          6
  12P GAIN WILD-TYPE                                                                                       31
                    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                                                                                       24
  PRIMARY TUMOR                                                                                            26
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 31
  REGIONAL LYMPH NODE                                                                                     102
D21V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      6   13
  12P GAIN WILD-TYPE   70  113
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                6                 70
  MALE                 13                113
D21V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   19
  12P GAIN WILD-TYPE    3  180
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 0                  3
  YES               19                180
                    vv
clus                  M0  M1 M1A M1B M1C
  12P GAIN MUTATED    16   1   1   0   0
  12P GAIN WILD-TYPE 160   1   1   2   3
D21V6, 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 104   2   6  14   1   3  13   5  16   5
D21V7, multiclass
D21V8, 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       14       20         9
                    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        22         6          5         17
                    vv
clus                 STAGE IIIC STAGE IV
  12P GAIN MUTATED            2        2
  12P GAIN WILD-TYPE         25        5
D21V9, multiclass

Clustering(22) Variable = 12q gain mutation analysis
D22V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    1  4
  12Q GAIN WILD-TYPE 58 51
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                109 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                 51 
$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        3.88        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-A3F8 TCGA-EB-A1NK 
       22.36         6.64        19.36         7.00        14.83         0.53 
TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF 
        0.43         1.35         1.28         1.18         0.30         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X 
        0.53         0.26         0.10         0.20         0.39        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-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-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-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL 
        4.18        28.64        42.84        78.44         6.58         1.71 
TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR 
       12.10        10.09         5.95        72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 
        0.13        15.35        24.85        15.35        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26C TCGA-GN-A26D 
       10.09        16.21        15.39         5.59        24.00        14.70 
TCGA-IH-A3EA 
       12.59 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             12.16               0.10 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             70.16              98.76 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             17.56              10.09 
[1] "12.2 - 70.2 (17.6)" "0.1 - 98.8 (10.1)" 
        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-D9-A3Z4 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "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-D9-A3Z4 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "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-D9-A3Z4 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D22V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12Q GAIN MUTATED                    1             0
  12Q GAIN WILD-TYPE                 26            26
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12Q GAIN MUTATED                                                                                          2
  12Q GAIN WILD-TYPE                                                                                       35
                    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                                                                                       26
  PRIMARY TUMOR                                                                                            26
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 35
  REGIONAL LYMPH NODE                                                                                     108
D22V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    6
  12Q GAIN WILD-TYPE   75  120
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                1                 75
  MALE                  6                120
D22V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0    7
  12Q GAIN WILD-TYPE    3  192
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 0                  3
  YES                7                192
                    vv
clus                  M0  M1 M1A M1B M1C
  12Q GAIN MUTATED     6   0   0   0   0
  12Q GAIN WILD-TYPE 170   2   2   2   3
D22V6, 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 109   2   6  16   1   4  14   6  18   5
D22V7, multiclass
D22V8, 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       15       19         9
                    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        23         8          5         20
                    vv
clus                 STAGE IIIC STAGE IV
  12Q GAIN MUTATED            1        0
  12Q GAIN WILD-TYPE         26        7
D22V9, multiclass

Clustering(23) Variable = 13q gain mutation analysis
D23V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED   10 11
  13Q GAIN WILD-TYPE 49 44
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                21                 93 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                11                 44 
$`13Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2JF TCGA-D3-A3CE TCGA-D9-A3Z4 TCGA-DA-A1I7 TCGA-DA-A3F3 
       16.47        30.87        13.32         3.88        36.69         7.00 
TCGA-EB-A24C TCGA-EB-A24D TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29P TCGA-EE-A29R 
        0.43         1.35         8.81         7.96        12.03         8.84 
TCGA-EE-A2A5 TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A3PL TCGA-FS-A4F2 
        9.67        12.99        28.64        42.84         1.71         3.22 
TCGA-FW-A3TU TCGA-GN-A267 TCGA-GN-A268 
        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-EB-A1NK TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC 
       17.56        14.83         0.53         1.28         1.18         0.30 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z 
        0.13         0.53         0.26         0.10         0.20         0.39 
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-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
        1.08        27.12         9.47         8.12         9.99         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-A1A1 TCGA-ER-A3ET TCGA-FR-A2OS 
        3.52        11.11         4.18        78.44         6.58        12.10 
TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 
       10.09         5.95        72.16        24.00         8.81        53.82 
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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A269 TCGA-GN-A26A 
       15.35        31.33        84.72        10.09         5.59        12.16 
TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       24.00        14.70        12.59 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.13               0.10 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             42.84              98.76 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              9.67              10.78 
[1] "0.1 - 42.8 (9.7)"  "0.1 - 98.8 (10.8)"
        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-D9-A3Z4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D23V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  13Q GAIN MUTATED                   10             3
  13Q GAIN WILD-TYPE                 17            23
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  13Q GAIN MUTATED                                                                                          7
  13Q GAIN WILD-TYPE                                                                                       30
                    vv
clus                 REGIONAL LYMPH NODE
  13Q GAIN MUTATED                    15
  13Q GAIN WILD-TYPE                  97
D23V3, multiclass
                                                                                          clus
vv                                                                                         13Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     10
  PRIMARY TUMOR                                                                                           3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                7
  REGIONAL LYMPH NODE                                                                                    15
                                                                                          clus
vv                                                                                         13Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       17
  PRIMARY TUMOR                                                                                            23
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                      97
D23V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     13   22
  13Q GAIN WILD-TYPE   63  104
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               13                 63
  MALE                 22                104
D23V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   35
  13Q GAIN WILD-TYPE    3  164
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 0                  3
  YES               35                164
                    vv
clus                  M0  M1 M1A M1B M1C
  13Q GAIN MUTATED    29   0   1   0   0
  13Q GAIN WILD-TYPE 147   2   1   2   3
D23V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  13Q GAIN MUTATED   15  0   4   5  0   0   3   0  2  1
  13Q GAIN WILD-TYPE 95  2   4  12  1   5  11   6 17  4
D23V7, multiclass
D23V8, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  13Q GAIN MUTATED             0       2        2        3        0         1
  13Q GAIN WILD-TYPE           4      15        8       12       20         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  13Q GAIN MUTATED           2         5         2          3          4
  13Q GAIN WILD-TYPE         8        18         7          4         17
                    vv
clus                 STAGE IIIC STAGE IV
  13Q GAIN MUTATED            4        1
  13Q GAIN WILD-TYPE         23        6
D23V9, multiclass

Clustering(24) Variable = 14q gain mutation analysis
D24V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED    2  6
  14Q GAIN WILD-TYPE 57 49
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                106 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 6                 49 
$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2.86         3.88        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       39.19         9.99        44.52        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A1NK 
        6.64        19.36         7.00        17.56        14.83         0.53 
TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF 
        0.43         1.35         1.28         1.18         0.30         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X 
        0.53         0.26         0.10         0.20         0.39        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-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-A19N 
        9.67         8.94         3.52        11.11         4.18        42.84 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN 
       78.44         6.58         1.71        12.10        10.09         5.95 
TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
       72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       15.35        31.33        84.72        10.09        16.21        15.39 
TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-IH-A3EA 
        5.59        12.16        24.00        12.59 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.08               0.10 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             36.69              98.76 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             14.19              10.09 
[1] "1.1 - 36.7 (14.2)" "0.1 - 98.8 (10.1)"
        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-D9-A3Z4 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED"   "14Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        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-D9-A3Z4 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED"   "14Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        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-D9-A3Z4 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED"   "14Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D24V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  14Q GAIN MUTATED                    2             0
  14Q GAIN WILD-TYPE                 25            26
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  14Q GAIN MUTATED                                                                                          3
  14Q GAIN WILD-TYPE                                                                                       34
                    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                                                                                       25
  PRIMARY TUMOR                                                                                            26
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 34
  REGIONAL LYMPH NODE                                                                                     103
D24V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      4   10
  14Q GAIN WILD-TYPE   72  116
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                4                 72
  MALE                 10                116
D24V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   14
  14Q GAIN WILD-TYPE    3  185
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 0                  3
  YES               14                185
                    vv
clus                  M0  M1 M1A M1B M1C
  14Q GAIN MUTATED    12   0   0   0   0
  14Q GAIN WILD-TYPE 164   2   2   2   3
D24V6, 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 101   2   8  17   1   4  12   6  18   5
D24V7, multiclass
D24V8, 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       14       18         9
                    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        21         9          7         19
                    vv
clus                 STAGE IIIC STAGE IV
  14Q GAIN MUTATED            2        0
  14Q GAIN WILD-TYPE         25        7
D24V9, multiclass

Clustering(25) Variable = 15q gain mutation analysis
D25V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    6 11
  15Q GAIN WILD-TYPE 53 44
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                17                 97 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                 44 
$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
        4.01         2.86         3.88        48.79        51.12        10.03 
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-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A1NK 
       22.36         6.64        19.36         7.00        14.83         0.53 
TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF 
        0.43         1.35         1.28         1.18         0.30         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X 
        0.53         0.26         0.10         0.20         0.39        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        6.31         1.12         1.35         4.27        36.07         5.13 
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-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        2.43         8.09        11.31        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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FS-A1ZN 
        6.58         1.71        12.10        10.09         5.95        24.00 
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-A263 TCGA-GN-A265 TCGA-GN-A266 
        0.13        15.35        24.85        15.35        84.72        10.09 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D 
       16.21        15.39         5.59        12.16        24.00        14.70 
TCGA-IH-A3EA 
       12.59 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              3.22               0.10 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             72.16              98.76 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             22.55               9.99 
[1] "3.2 - 72.2 (22.6)" "0.1 - 98.8 (10.0)"
        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-D9-A3Z4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "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                 22            26
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  15Q GAIN MUTATED                                                                                          5
  15Q GAIN WILD-TYPE                                                                                       32
                    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                                                                                       22
  PRIMARY TUMOR                                                                                            26
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                      96
D25V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     10   16
  15Q GAIN WILD-TYPE   66  110
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               10                 66
  MALE                 16                110
D25V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   26
  15Q GAIN WILD-TYPE    3  173
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 0                  3
  YES               26                173
                    vv
clus                  M0  M1 M1A M1B M1C
  15Q GAIN MUTATED    24   0   0   0   0
  15Q GAIN WILD-TYPE 152   2   2   2   3
D25V6, 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 95  2   8  13  1   3  13   6 17  5
D25V7, multiclass
D25V8, 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       13       18         8
                    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        21         8          7         17
                    vv
clus                 STAGE IIIC STAGE IV
  15Q GAIN MUTATED            3        0
  15Q GAIN WILD-TYPE         24        7
D25V9, multiclass

Clustering(26) Variable = 16p gain mutation analysis
D26V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    2  6
  16P GAIN WILD-TYPE 57 49
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 8                106 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                 49 
$`16P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3CE TCGA-EB-A1NK TCGA-EE-A20H TCGA-EE-A29R TCGA-EE-A2A5 
       70.16        13.32         0.53         8.81         8.84         9.67 
TCGA-ER-A19D TCGA-ER-A19M 
        3.52        28.64 

$`16P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        32.55        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        3.88        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-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF 
        0.43         1.35         1.28         1.18         0.30         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X 
        0.53         0.26         0.10         0.20         0.39        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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A 
        6.58         1.71        12.10        10.09         5.95        72.16 
TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC 
       24.00         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-A263 
        0.20         1.02         0.13        15.35        24.85        15.35 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 
       31.33        84.72        10.09        16.21        15.39         5.59 
TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       12.16        24.00        14.70        12.59 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.53               0.10 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             70.16              98.76 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             9.255             10.945 
[1] "0.5 - 70.2 (9.3)"  "0.1 - 98.8 (10.9)"
        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-D9-A3Z4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D26V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16P GAIN MUTATED                    2             1
  16P GAIN WILD-TYPE                 25            25
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16P GAIN MUTATED                                                                                          5
  16P GAIN WILD-TYPE                                                                                       32
                    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                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                     6
                                                                                          clus
vv                                                                                         16P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       25
  PRIMARY TUMOR                                                                                            25
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                     106
D26V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5    9
  16P GAIN WILD-TYPE   71  117
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                5                 71
  MALE                  9                117
D26V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   14
  16P GAIN WILD-TYPE    3  185
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 0                  3
  YES               14                185
                    vv
clus                  M0  M1 M1A M1B M1C
  16P GAIN MUTATED    14   0   0   0   0
  16P GAIN WILD-TYPE 162   2   2   2   3
D26V6, multiclass
                    vv
clus                  N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  16P GAIN MUTATED    10   0   1   3   0   0   0   0   0   0
  16P GAIN WILD-TYPE 100   2   7  14   1   5  14   6  19   5
D26V7, multiclass
D26V8, 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       12       20         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16P GAIN MUTATED           1         2         2          1          0
  16P GAIN WILD-TYPE         9        21         7          6         21
                    vv
clus                 STAGE IIIC STAGE IV
  16P GAIN MUTATED            1        0
  16P GAIN WILD-TYPE         26        7
D26V9, multiclass

Clustering(27) Variable = 16q gain mutation analysis
D27V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    2  5
  16Q GAIN WILD-TYPE 57 50
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                107 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                 50 
$`16Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3CE TCGA-EB-A1NK TCGA-EE-A20H TCGA-EE-A29R TCGA-ER-A19D 
       70.16        13.32         0.53         8.81         8.84         3.52 
TCGA-ER-A19M 
       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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        3.88        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-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF 
        0.43         1.35         1.28         1.18         0.30         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X 
        0.53         0.26         0.10         0.20         0.39        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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN 
       78.44         6.58         1.71        12.10        10.09         5.95 
TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
       72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       15.35        31.33        84.72        10.09        16.21        15.39 
TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
        5.59        12.16        24.00        14.70        12.59 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.53               0.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             70.16              98.76 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              8.84              10.78 
[1] "0.5 - 70.2 (8.8)"  "0.1 - 98.8 (10.8)"
        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-D9-A3Z4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D27V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16Q GAIN MUTATED                    2             1
  16Q GAIN WILD-TYPE                 25            25
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16Q GAIN MUTATED                                                                                          4
  16Q GAIN WILD-TYPE                                                                                       33
                    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                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                     6
                                                                                          clus
vv                                                                                         16Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       25
  PRIMARY TUMOR                                                                                            25
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 33
  REGIONAL LYMPH NODE                                                                                     106
D27V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4    9
  16Q GAIN WILD-TYPE   72  117
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                4                 72
  MALE                  9                117
D27V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   13
  16Q GAIN WILD-TYPE    3  186
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 0                  3
  YES               13                186
                    vv
clus                  M0  M1 M1A M1B M1C
  16Q GAIN MUTATED    13   0   0   0   0
  16Q GAIN WILD-TYPE 163   2   2   2   3
D27V6, multiclass
                    vv
clus                  N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  16Q GAIN MUTATED     8   0   1   4   0   0   0   0   0   0
  16Q GAIN WILD-TYPE 102   2   7  13   1   5  14   6  19   5
D27V7, multiclass
D27V8, 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       13       20         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16Q GAIN MUTATED           1         2         2          1          1
  16Q GAIN WILD-TYPE         9        21         7          6         20
                    vv
clus                 STAGE IIIC STAGE IV
  16Q GAIN MUTATED            1        0
  16Q GAIN WILD-TYPE         26        7
D27V9, multiclass

Clustering(28) Variable = 17p gain mutation analysis
D28V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    7  4
  17P GAIN WILD-TYPE 52 51
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                11                103 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 4                 51 
$`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-D9-A3Z4 
       45.70        24.00         9.30         4.01         2.86         3.88 
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-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        44.52        25.15        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D 
        7.00        17.56        14.83         0.53         0.43         1.35 
TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A 
        1.28         1.18         0.30         0.13         0.53         0.26 
TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        0.10         0.20         0.39        11.57         6.31         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
        1.35        12.20         4.27        36.07         8.81         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-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-ER-A19D TCGA-ER-A19F 
       11.31        25.28        23.90         9.67         3.52        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
        4.18        12.99        28.64        42.84        78.44         6.58 
TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR 
       12.10        10.09         5.95        72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 
        0.13        15.35        24.85        15.35        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C 
       10.09        16.21        15.39         5.59        12.16        24.00 
TCGA-IH-A3EA 
       12.59 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.71               0.10 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             36.69              98.76 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              9.47              10.78 
[1] "1.7 - 36.7 (9.5)"  "0.1 - 98.8 (10.8)"
        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-D9-A3Z4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        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-D9-A3Z4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        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-D9-A3Z4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17P GAIN MUTATED                    1             0
  17P GAIN WILD-TYPE                 26            26
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17P GAIN MUTATED                                                                                          5
  17P GAIN WILD-TYPE                                                                                       32
                    vv
clus                 REGIONAL LYMPH NODE
  17P GAIN MUTATED                     9
  17P GAIN WILD-TYPE                 103
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                                                                                     9
                                                                                          clus
vv                                                                                         17P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       26
  PRIMARY TUMOR                                                                                            26
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                     103
D28V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      8    7
  17P GAIN WILD-TYPE   68  119
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                8                 68
  MALE                  7                119
D28V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   15
  17P GAIN WILD-TYPE    3  184
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 0                  3
  YES               15                184
                    vv
clus                  M0  M1 M1A M1B M1C
  17P GAIN MUTATED    12   0   1   0   0
  17P GAIN WILD-TYPE 164   2   1   2   3
D28V6, multiclass
                    vv
clus                  N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  17P GAIN MUTATED     9   0   0   2   0   1   1   0   1   0
  17P GAIN WILD-TYPE 101   2   8  15   1   4  13   6  18   5
D28V7, multiclass
D28V8, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17P GAIN MUTATED             0       0        2        0        1         1
  17P GAIN WILD-TYPE           4      17        8       15       19         8
                    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        20         8          7         18
                    vv
clus                 STAGE IIIC STAGE IV
  17P GAIN MUTATED            1        1
  17P GAIN WILD-TYPE         26        6
D28V9, multiclass

Clustering(29) Variable = 17q gain mutation analysis
D29V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    8  9
  17Q GAIN WILD-TYPE 51 46
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                17                 97 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 9                 46 
$`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-D9-A3Z4 
       45.70        24.00         9.30         4.01         2.86         3.88 
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-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
        9.99        44.52        25.15        22.36        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV 
       17.56        14.83         0.53         0.43         1.35         1.28 
TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B 
        1.18         0.30         0.13         0.53         0.26         0.10 
TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
        0.20         0.39        11.57         6.31         1.35        12.20 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       36.07         8.81         7.96        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        4.41        27.12         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-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        3.52        11.11         4.18        12.99        28.64        42.84 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A44A TCGA-FS-A1ZN 
       78.44         6.58        12.10        10.09        72.16        24.00 
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-A263 TCGA-GN-A264 
        1.02         0.13        15.35        24.85        15.35        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C 
       84.72        10.09        16.21         5.59        12.16        24.00 
TCGA-IH-A3EA 
       12.59 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              1.08               0.10 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             36.69              98.76 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              6.64              11.15 
[1] "1.1 - 36.7 (6.6)"  "0.1 - 98.8 (11.2)"
        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-D9-A3Z4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        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-D9-A3Z4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        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-D9-A3Z4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D29V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17Q GAIN MUTATED                    2             0
  17Q GAIN WILD-TYPE                 25            26
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17Q GAIN MUTATED                                                                                          5
  17Q GAIN WILD-TYPE                                                                                       32
                    vv
clus                 REGIONAL LYMPH NODE
  17Q GAIN MUTATED                    17
  17Q GAIN WILD-TYPE                  95
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                                                                                    17
                                                                                          clus
vv                                                                                         17Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       25
  PRIMARY TUMOR                                                                                            26
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                      95
D29V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     12   12
  17Q GAIN WILD-TYPE   64  114
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               12                 64
  MALE                 12                114
D29V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   24
  17Q GAIN WILD-TYPE    3  175
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 0                  3
  YES               24                175
                    vv
clus                  M0  M1 M1A M1B M1C
  17Q GAIN MUTATED    21   0   1   0   0
  17Q GAIN WILD-TYPE 155   2   1   2   3
D29V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  17Q GAIN MUTATED   14  0   0   2  0   2   1   1  3  0
  17Q GAIN WILD-TYPE 96  2   8  15  1   3  13   5 16  5
D29V7, multiclass
D29V8, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17Q GAIN MUTATED             0       0        2        1        3         1
  17Q GAIN WILD-TYPE           4      17        8       14       17         8
                    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        19         8          7         17
                    vv
clus                 STAGE IIIC STAGE IV
  17Q GAIN MUTATED            3        1
  17Q GAIN WILD-TYPE         24        6
D29V9, multiclass

Clustering(30) Variable = 18p gain mutation analysis
D30V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    6 10
  18P GAIN WILD-TYPE 53 45
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                16                 98 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                10                 45 
$`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-EB-A41A TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-FS-A4F2 
        0.26         1.12        38.63         1.08        12.03         3.22 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D 
       16.21        12.16        24.00        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-D9-A3Z4 TCGA-DA-A1HV 
        9.30         5.39         4.01         2.86         3.88        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       35.80        51.12        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV 
       17.56        14.83         0.53         0.43         1.35         1.28 
TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41B TCGA-EB-A42Y 
        1.18         0.30         0.13         0.53         0.10         0.20 
TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
        0.39        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-A2OS 
       28.64        42.84        78.44         6.58         1.71        12.10 
TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 
       10.09         5.95        72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       24.85        15.35        31.33        84.72        10.09        15.39 
TCGA-GN-A269 TCGA-IH-A3EA 
        5.59        12.59 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.26               0.10 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             45.70              98.76 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             14.01              10.04 
[1] "0.3 - 45.7 (14.0)" "0.1 - 98.8 (10.0)"
        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-D9-A3Z4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        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-D9-A3Z4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        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-D9-A3Z4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D30V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18P GAIN MUTATED                    5             2
  18P GAIN WILD-TYPE                 22            24
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18P GAIN MUTATED                                                                                          5
  18P GAIN WILD-TYPE                                                                                       32
                    vv
clus                 REGIONAL LYMPH NODE
  18P GAIN MUTATED                    13
  18P GAIN WILD-TYPE                  99
D30V3, multiclass
                                                                                          clus
vv                                                                                         18P GAIN MUTATED
  DISTANT METASTASIS                                                                                      5
  PRIMARY TUMOR                                                                                           2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    13
                                                                                          clus
vv                                                                                         18P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       22
  PRIMARY TUMOR                                                                                            24
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                      99
D30V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     12   13
  18P GAIN WILD-TYPE   64  113
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               12                 64
  MALE                 13                113
D30V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1   24
  18P GAIN WILD-TYPE    2  175
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 1                  2
  YES               24                175
                    vv
clus                  M0  M1 M1A M1B M1C
  18P GAIN MUTATED    22   0   1   0   0
  18P GAIN WILD-TYPE 154   2   1   2   3
D30V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  18P GAIN MUTATED   14  0   3   2  0   1   1   0  3  0
  18P GAIN WILD-TYPE 96  2   5  15  1   4  13   6 16  5
D30V7, multiclass
D30V8, 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       15       18         9
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18P GAIN MUTATED           0         7         1          3          2
  18P GAIN WILD-TYPE        10        16         8          4         19
                    vv
clus                 STAGE IIIC STAGE IV
  18P GAIN MUTATED            4        0
  18P GAIN WILD-TYPE         23        7
D30V9, multiclass

Clustering(31) Variable = 18q gain mutation analysis
D31V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    5  5
  18Q GAIN WILD-TYPE 54 50
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                104 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 50 
$`18Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3CC TCGA-DA-A1I1 TCGA-EB-A41A TCGA-EE-A29L TCGA-FS-A4F2 
       32.55        45.70        39.19         0.26         1.08         3.22 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D TCGA-IH-A3EA 
       16.21        12.16        14.70        12.59 

$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        3.88        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-EB-A1NK 
        6.64        19.36         7.00        17.56        14.83         0.53 
TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF 
        0.43         1.35         1.28         1.18         0.30         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z 
        0.53         0.10         0.20         0.39        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-A2OS 
       28.64        42.84        78.44         6.58         1.71        12.10 
TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 
       10.09         5.95        72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       24.85        15.35        31.33        84.72        10.09        15.39 
TCGA-GN-A269 TCGA-GN-A26C 
        5.59        24.00 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.26               0.10 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             45.70              98.76 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            13.645             10.090 
[1] "0.3 - 45.7 (13.6)" "0.1 - 98.8 (10.1)"
        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-D9-A3Z4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
[1] "hr=" "1.2"
D31V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18Q GAIN MUTATED                    4             2
  18Q GAIN WILD-TYPE                 23            24
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18Q GAIN MUTATED                                                                                          4
  18Q GAIN WILD-TYPE                                                                                       33
                    vv
clus                 REGIONAL LYMPH NODE
  18Q GAIN MUTATED                     5
  18Q GAIN WILD-TYPE                 107
D31V3, multiclass
                                                                                          clus
vv                                                                                         18Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      4
  PRIMARY TUMOR                                                                                           2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         18Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       23
  PRIMARY TUMOR                                                                                            24
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 33
  REGIONAL LYMPH NODE                                                                                     107
D31V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7    8
  18Q GAIN WILD-TYPE   69  118
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                7                 69
  MALE                  8                118
D31V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   15
  18Q GAIN WILD-TYPE    3  184
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 0                  3
  YES               15                184
                    vv
clus                  M0  M1 M1A M1B M1C
  18Q GAIN MUTATED    13   0   0   0   0
  18Q GAIN WILD-TYPE 163   2   2   2   3
D31V6, multiclass
                    vv
clus                  N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  18Q GAIN MUTATED    10   0   2   0   0   0   0   0   2   0
  18Q GAIN WILD-TYPE 100   2   6  17   1   5  14   6  17   5
D31V7, multiclass
D31V8, 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       15       20         9
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18Q GAIN MUTATED           0         7         0          2          0
  18Q GAIN WILD-TYPE        10        16         9          5         21
                    vv
clus                 STAGE IIIC STAGE IV
  18Q GAIN MUTATED            2        0
  18Q GAIN WILD-TYPE         25        7
D31V9, multiclass

Clustering(32) Variable = 19p gain mutation analysis
D32V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    1  3
  19P GAIN WILD-TYPE 58 52
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                110 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                 52 
$`19P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-EE-A29L TCGA-EE-A29R TCGA-GN-A26C 
       32.55         1.08         8.84        24.00 

$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2.86         3.88        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
       14.83         0.53         0.43         1.35         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y 
        0.30         0.13         0.53         0.26         0.10         0.20 
TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.39        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-A29M TCGA-EE-A29N TCGA-EE-A29P 
       11.15        38.63         4.41        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-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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN 
        1.71        12.10        10.09         5.95        72.16        24.00 
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-A263 TCGA-GN-A264 
        1.02         0.13        15.35        24.85        15.35        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A 
       84.72        10.09        16.21        15.39         5.59        12.16 
TCGA-GN-A26D TCGA-IH-A3EA 
       14.70        12.59 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              1.08               0.10 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             32.55              98.76 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             16.42              10.52 
[1] "1.1 - 32.5 (16.4)" "0.1 - 98.8 (10.5)"
        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-D9-A3Z4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D32V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19P GAIN MUTATED                    4             1
  19P GAIN WILD-TYPE                 23            25
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19P GAIN MUTATED                                                                                          0
  19P GAIN WILD-TYPE                                                                                       37
                    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                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         19P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       23
  PRIMARY TUMOR                                                                                            25
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 37
  REGIONAL LYMPH NODE                                                                                     105
D32V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      5    7
  19P GAIN WILD-TYPE   71  119
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                5                 71
  MALE                  7                119
D32V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   11
  19P GAIN WILD-TYPE    2  188
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 1                  2
  YES               11                188
                    vv
clus                  M0  M1 M1A M1B M1C
  19P GAIN MUTATED    11   0   0   0   0
  19P GAIN WILD-TYPE 165   2   2   2   3
D32V6, multiclass
                    vv
clus                  N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  19P GAIN MUTATED     8   0   0   1   0   0   1   0   1   0
  19P GAIN WILD-TYPE 102   2   8  16   1   5  13   6  18   5
D32V7, multiclass
D32V8, 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       14       20         8
                    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        22         9          7         21
                    vv
clus                 STAGE IIIC STAGE IV
  19P GAIN MUTATED            3        0
  19P GAIN WILD-TYPE         24        7
D32V9, multiclass

Clustering(33) Variable = 19q gain mutation analysis
D33V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    3  4
  19Q GAIN WILD-TYPE 56 51
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                107 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                 51 
$`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-D9-A3Z4 
       24.00         9.30         5.39         4.01         2.86         3.88 
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-EB-A1NK 
        6.64        19.36         7.00        17.56        14.83         0.53 
TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF 
        0.43         1.35         1.28         1.18         0.30         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X 
        0.53         0.26         0.10         0.20         0.39        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-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        4.41        27.12         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-A19M 
        8.94         3.52        11.11         4.18        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3PL TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN 
       42.84        78.44         1.71        12.10        10.09         5.95 
TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
       72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       15.35        31.33        84.72        10.09        16.21        15.39 
TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
        5.59        12.16        24.00        14.70        12.59 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              1.08               0.10 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             32.55              98.76 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              8.84              10.78 
[1] "1.1 - 32.5 (8.8)"  "0.1 - 98.8 (10.8)"
        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-D9-A3Z4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "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                 23            26
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19Q GAIN MUTATED                                                                                          2
  19Q GAIN WILD-TYPE                                                                                       35
                    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                                                                                       23
  PRIMARY TUMOR                                                                                            26
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 35
  REGIONAL LYMPH NODE                                                                                     103
D33V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      9    6
  19Q GAIN WILD-TYPE   67  120
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                9                 67
  MALE                  6                120
D33V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0   15
  19Q GAIN WILD-TYPE    3  184
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 0                  3
  YES               15                184
                    vv
clus                  M0  M1 M1A M1B M1C
  19Q GAIN MUTATED    14   0   0   0   0
  19Q GAIN WILD-TYPE 162   2   2   2   3
D33V6, 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 102   2   7  15   1   5  14   6  17   4
D33V7, multiclass
D33V8, 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       14       20         8
                    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        22         8          6         21
                    vv
clus                 STAGE IIIC STAGE IV
  19Q GAIN MUTATED            3        0
  19Q GAIN WILD-TYPE         24        7
D33V9, multiclass

Clustering(34) Variable = 20p gain mutation analysis
D34V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   12 16
  20P GAIN WILD-TYPE 47 39
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                28                 86 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                16                 39 
$`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-EB-A24D TCGA-EE-A20B 
       10.03        13.68        36.69        17.56         1.35        36.07 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.81         7.96         8.84        25.28         9.67         8.94 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-FR-A3YN TCGA-FS-A4F2 TCGA-FW-A3I3 
        4.18        12.99        28.64         5.95         3.22         0.20 
TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D 
       31.33        12.16        24.00        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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        4.01         2.86         3.88        48.79        35.80        51.12 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       39.19         9.99        44.52        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A1NK TCGA-EB-A24C 
        6.64        19.36         7.00        14.83         0.53         0.43 
TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A 
        1.28         1.18         0.30         0.13         0.53         0.26 
TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        0.10         0.20         0.39        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-A2OS TCGA-FR-A3R1 TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR 
        1.71        12.10        10.09        72.16        24.00         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-A263 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        15.35        84.72        10.09        16.21        15.39 
TCGA-GN-A269 TCGA-IH-A3EA 
        5.59        12.59 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               0.2                0.1 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             36.69              98.76 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            13.155             10.090 
[1] "0.2 - 36.7 (13.2)" "0.1 - 98.8 (10.1)"
        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-D9-A3Z4 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        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-D9-A3Z4 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        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-D9-A3Z4 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D34V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20P GAIN MUTATED                   10             4
  20P GAIN WILD-TYPE                 17            22
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20P GAIN MUTATED                                                                                         12
  20P GAIN WILD-TYPE                                                                                       25
                    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                                                                                           4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               12
  REGIONAL LYMPH NODE                                                                                    31
                                                                                          clus
vv                                                                                         20P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       17
  PRIMARY TUMOR                                                                                            22
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 25
  REGIONAL LYMPH NODE                                                                                      81
D34V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     19   38
  20P GAIN WILD-TYPE   57   88
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               19                 57
  MALE                 38                 88
D34V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1   56
  20P GAIN WILD-TYPE    2  143
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 1                  2
  YES               56                143
                    vv
clus                  M0  M1 M1A M1B M1C
  20P GAIN MUTATED    50   2   1   0   0
  20P GAIN WILD-TYPE 126   0   1   2   3
D34V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  20P GAIN MUTATED   33  0   4   3  0   2   5   2  4  1
  20P GAIN WILD-TYPE 77  2   4  14  1   3   9   4 15  4
D34V7, multiclass
D34V8, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  20P GAIN MUTATED             2       6        6        5        5         2
  20P GAIN WILD-TYPE           2      11        4       10       15         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  20P GAIN MUTATED           1         5         2          3          6
  20P GAIN WILD-TYPE         9        18         7          4         15
                    vv
clus                 STAGE IIIC STAGE IV
  20P GAIN MUTATED            8        2
  20P GAIN WILD-TYPE         19        5
D34V9, multiclass

Clustering(35) Variable = 20q gain mutation analysis
D35V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   17 18
  20Q GAIN WILD-TYPE 42 37
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                35                 79 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                18                 37 
$`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-EB-A24D TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29L 
        1.35        36.07         8.81         7.96        38.63         1.08 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19J 
       12.03         8.84        25.28         9.67         8.94         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F2 
       12.99        28.64         1.71         5.95        72.16         3.22 
TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D 
        0.20        31.33        12.16        24.00        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-D9-A3Z4 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
        4.01         2.86         3.88        35.80        51.12        39.19 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        44.52        25.15        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XB 
        7.00        14.83         0.53         0.43         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y 
        0.30         0.13         0.53         0.26         0.10         0.20 
TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.39        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-FR-A2OS TCGA-FR-A3R1 TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 
        6.58        12.10        10.09        24.00         8.81        53.82 
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-A263 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 
       15.35        84.72        10.09        16.21        15.39         5.59 
TCGA-IH-A3EA 
       12.59 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               0.2                0.1 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             72.16              98.76 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             12.99              10.09 
[1] "0.2 - 72.2 (13.0)" "0.1 - 98.8 (10.1)"
        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-D9-A3Z4 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        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-D9-A3Z4 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        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-D9-A3Z4 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20Q GAIN MUTATED                   12             5
  20Q GAIN WILD-TYPE                 15            21
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20Q GAIN MUTATED                                                                                         14
  20Q GAIN WILD-TYPE                                                                                       23
                    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                                                                                           5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               14
  REGIONAL LYMPH NODE                                                                                    39
                                                                                          clus
vv                                                                                         20Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       15
  PRIMARY TUMOR                                                                                            21
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 23
  REGIONAL LYMPH NODE                                                                                      73
D35V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     24   46
  20Q GAIN WILD-TYPE   52   80
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               24                 52
  MALE                 46                 80
D35V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      1   69
  20Q GAIN WILD-TYPE    2  130
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 1                  2
  YES               69                130
                    vv
clus                  M0  M1 M1A M1B M1C
  20Q GAIN MUTATED    59   2   2   1   0
  20Q GAIN WILD-TYPE 117   0   0   1   3
D35V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  20Q GAIN MUTATED   38  0   4   6  0   2   6   2  6  1
  20Q GAIN WILD-TYPE 72  2   4  11  1   3   8   4 13  4
D35V7, multiclass
D35V8, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  20Q GAIN MUTATED             2       6        6        5        7         3
  20Q GAIN WILD-TYPE           2      11        4       10       13         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  20Q GAIN MUTATED           1         6         3          3          9
  20Q GAIN WILD-TYPE         9        17         6          4         12
                    vv
clus                 STAGE IIIC STAGE IV
  20Q GAIN MUTATED            9        3
  20Q GAIN WILD-TYPE         18        4
D35V9, multiclass

Clustering(36) Variable = 21q gain mutation analysis
D36V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    7  8
  21Q GAIN WILD-TYPE 52 47
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                15                 99 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 8                 47 
$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2.86         3.88        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
       14.83         0.53         0.43         1.35         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y 
        0.30         0.13         0.53         0.26         0.10         0.20 
TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.39        11.57         6.31         1.12         1.35        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        4.27        36.07         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-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-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F 
        6.48         2.43         8.09        23.90         8.94        11.11 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A2OS 
        4.18        28.64        42.84        78.44         6.58        12.10 
TCGA-FR-A3R1 TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 
       10.09        72.16        24.00         8.81        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A263 
        6.41         1.02         0.13        15.35        24.85        15.35 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 
       31.33        84.72        10.09        16.21        15.39         5.59 
TCGA-GN-A26A TCGA-GN-A26C TCGA-IH-A3EA 
       12.16        24.00        12.59 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               0.2                0.1 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             25.28              98.76 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              7.96              11.41 
[1] "0.2 - 25.3 (8.0)"  "0.1 - 98.8 (11.4)"
        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-D9-A3Z4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED"   "21Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        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-D9-A3Z4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED"   "21Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        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-D9-A3Z4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED"   "21Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
[1] "hr=" "2.5"
D36V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  21Q GAIN MUTATED                    4             1
  21Q GAIN WILD-TYPE                 23            25
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  21Q GAIN MUTATED                                                                                          6
  21Q GAIN WILD-TYPE                                                                                       31
                    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                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                    11
                                                                                          clus
vv                                                                                         21Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       23
  PRIMARY TUMOR                                                                                            25
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 31
  REGIONAL LYMPH NODE                                                                                     101
D36V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     10   12
  21Q GAIN WILD-TYPE   66  114
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               10                 66
  MALE                 12                114
D36V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   22
  21Q GAIN WILD-TYPE    3  177
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 0                  3
  YES               22                177
                    vv
clus                  M0  M1 M1A M1B M1C
  21Q GAIN MUTATED    18   1   1   0   0
  21Q GAIN WILD-TYPE 158   1   1   2   3
D36V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  21Q GAIN MUTATED   16  0   1   1  0   2   0   0  1  0
  21Q GAIN WILD-TYPE 94  2   7  16  1   3  14   6 18  5
D36V7, multiclass
D36V8, 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       11       19         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  21Q GAIN MUTATED           0         4         0          2          1
  21Q GAIN WILD-TYPE        10        19         9          5         20
                    vv
clus                 STAGE IIIC STAGE IV
  21Q GAIN MUTATED            2        2
  21Q GAIN WILD-TYPE         25        5
D36V9, multiclass

Clustering(37) Variable = 22q gain mutation analysis
D37V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   16 15
  22Q GAIN WILD-TYPE 43 40
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                31                 83 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                15                 40 
$`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-EB-A1NK TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R 
        0.53         8.81         1.08        27.12         9.47         8.84 
TCGA-ER-A19M TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F2 TCGA-FW-A3I3 
       28.64         6.58         5.95        72.16         3.22         0.20 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D 
       31.33        84.72        16.21        12.16        24.00        14.70 
TCGA-IH-A3EA 
       12.59 

$`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-D9-A3Z4 TCGA-DA-A1HW 
       13.32        24.00         4.01         2.86         3.88        35.80 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 
       51.12        13.68         9.99        44.52         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
        7.00        14.83         0.43         1.35         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y 
        0.30         0.13         0.53         0.26         0.10         0.20 
TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.39        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-FR-A2OS TCGA-FR-A3R1 TCGA-FS-A1ZN TCGA-FS-A1ZR 
       78.44         1.71        12.10        10.09        24.00         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-A263 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A269 
       24.85        15.35        10.09        15.39         5.59 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               0.2                0.1 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             84.72              98.76 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             14.70              10.09 
[1] "0.2 - 84.7 (14.7)" "0.1 - 98.8 (10.1)"
        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-D9-A3Z4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
[1] "hr=" "1.3"
D37V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  22Q GAIN MUTATED                    8             5
  22Q GAIN WILD-TYPE                 19            21
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  22Q GAIN MUTATED                                                                                         13
  22Q GAIN WILD-TYPE                                                                                       24
                    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                                                                                           5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               13
  REGIONAL LYMPH NODE                                                                                    24
                                                                                          clus
vv                                                                                         22Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       19
  PRIMARY TUMOR                                                                                            21
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 24
  REGIONAL LYMPH NODE                                                                                      88
D37V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     22   28
  22Q GAIN WILD-TYPE   54   98
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               22                 54
  MALE                 28                 98
D37V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   49
  22Q GAIN WILD-TYPE    2  150
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 1                  2
  YES               49                150
                    vv
clus                  M0  M1 M1A M1B M1C
  22Q GAIN MUTATED    43   1   1   1   0
  22Q GAIN WILD-TYPE 133   1   1   1   3
D37V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  22Q GAIN MUTATED   23  0   4   3  0   3   4   3  7  0
  22Q GAIN WILD-TYPE 87  2   4  14  1   2  10   3 12  5
D37V7, multiclass
D37V8, 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         4
  22Q GAIN WILD-TYPE           4      14        9       12       16         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  22Q GAIN MUTATED           0         6         3          5          6
  22Q GAIN WILD-TYPE        10        17         6          2         15
                    vv
clus                 STAGE IIIC STAGE IV
  22Q GAIN MUTATED            9        1
  22Q GAIN WILD-TYPE         18        6
D37V9, multiclass

Clustering(38) Variable = Xq gain mutation analysis
D38V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED    0  1
  XQ GAIN WILD-TYPE 59 54
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1               113 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                54 
$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        4.01         2.86         3.88        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV 
       17.56        14.83         0.53         0.43         1.35         1.28 
TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B 
        1.18         0.30         0.13         0.53         0.26         0.10 
TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        0.20         0.39        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-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-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-A2OS TCGA-FR-A3R1 
       42.84        78.44         6.58         1.71        12.10        10.09 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 
        5.95        72.16        24.00         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-A263 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        15.35        84.72        10.09        16.21        15.39 
TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
        5.59        12.16        24.00        14.70        12.59 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            31.33              0.10 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            31.33             98.76 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            31.33             10.26 
[1] "31.3 - 31.3 (31.3)" "0.1 - 98.8 (10.3)" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1               113 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       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-A269        TCGA-GN-A26A        TCGA-GN-A26C        TCGA-GN-A26D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IH-A3EA 
"XQ GAIN WILD-TYPE" 
D38V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  XQ GAIN MUTATED                    1             1
  XQ GAIN WILD-TYPE                 26            25
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  XQ GAIN MUTATED                                                                                          1
  XQ GAIN WILD-TYPE                                                                                       36
                   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                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    1
                                                                                          clus
vv                                                                                         XQ GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      26
  PRIMARY TUMOR                                                                                           25
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                36
  REGIONAL LYMPH NODE                                                                                    111
D38V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1    3
  XQ GAIN WILD-TYPE   75  123
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               1                75
  MALE                 3               123
D38V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    4
  XQ GAIN WILD-TYPE    3  195
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                0                 3
  YES               4               195
                   vv
clus                 M0  M1 M1A M1B M1C
  XQ GAIN MUTATED     3   0   0   0   0
  XQ GAIN WILD-TYPE 173   2   2   2   3
D38V6, multiclass
                   vv
clus                 N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  XQ GAIN MUTATED     3   0   0   0   0   0   0   0   0   0
  XQ GAIN WILD-TYPE 107   2   8  17   1   5  14   6  19   5
D38V7, multiclass
D38V8, 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         1
  XQ GAIN WILD-TYPE           4      17        9       15       19         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        23         9          7         21
                   vv
clus                STAGE IIIC STAGE IV
  XQ GAIN MUTATED            0        0
  XQ GAIN WILD-TYPE         27        7
D38V9, multiclass

Clustering(39) Variable = 1p loss mutation analysis
D39V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    5  4
  1P LOSS WILD-TYPE 54 51
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                9               105 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4                51 
$`1P LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A3CC TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-EB-A24C TCGA-EE-A20H 
       22.55        45.70        13.68        36.69         0.43         8.81 
TCGA-EE-A29R TCGA-ER-A19L TCGA-GN-A26D 
        8.84        12.99        14.70 

$`1P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 
       16.47        32.55        70.16        98.76        28.08        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        3.88        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-EB-A1NK TCGA-EB-A24D 
       19.36         7.00        17.56        14.83         0.53         1.35 
TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A 
        1.28         1.18         0.30         0.13         0.53         0.26 
TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        0.10         0.20         0.39        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-A29S TCGA-EE-A29T TCGA-EE-A29V 
        9.47        12.03         8.12         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-A19M TCGA-ER-A19N TCGA-ER-A1A1 
        3.52        11.11         4.18        28.64        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A 
        6.58         1.71        12.10        10.09         5.95        72.16 
TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC 
       24.00         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-A263 
        0.20         1.02         0.13        15.35        24.85        15.35 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 
       31.33        84.72        10.09        16.21        15.39         5.59 
TCGA-GN-A26A TCGA-GN-A26C TCGA-IH-A3EA 
       12.16        24.00        12.59 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.43              0.10 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            45.70             98.76 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            13.68             10.09 
[1] "0.4 - 45.7 (13.7)" "0.1 - 98.8 (10.1)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D39V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1P LOSS MUTATED                    1             2
  1P LOSS WILD-TYPE                 26            24
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1P LOSS MUTATED                                                                                          4
  1P LOSS WILD-TYPE                                                                                       33
                   vv
clus                REGIONAL LYMPH NODE
  1P LOSS MUTATED                     9
  1P LOSS WILD-TYPE                 103
D39V3, multiclass
                                                                                          clus
vv                                                                                         1P LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                    9
                                                                                          clus
vv                                                                                         1P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      26
  PRIMARY TUMOR                                                                                           24
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                33
  REGIONAL LYMPH NODE                                                                                    103
D39V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      7    9
  1P LOSS WILD-TYPE   69  117
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               7                69
  MALE                 9               117
D39V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   16
  1P LOSS WILD-TYPE    3  183
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                0                 3
  YES              16               183
                   vv
clus                 M0  M1 M1A M1B M1C
  1P LOSS MUTATED    13   0   0   0   0
  1P LOSS WILD-TYPE 163   2   2   2   3
D39V6, multiclass
                   vv
clus                 N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  1P LOSS MUTATED     8   0   0   1   0   1   3   0   0   1
  1P LOSS WILD-TYPE 102   2   8  16   1   4  11   6  19   4
D39V7, multiclass
D39V8, 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         1
  1P LOSS WILD-TYPE           4      16       10       15       16         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1P LOSS MUTATED           0         3         1          0          2
  1P LOSS WILD-TYPE        10        20         8          7         19
                   vv
clus                STAGE IIIC STAGE IV
  1P LOSS MUTATED            2        0
  1P LOSS WILD-TYPE         25        7
D39V9, multiclass

Clustering(40) Variable = 1q loss mutation analysis
D40V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    1  4
  1Q LOSS WILD-TYPE 58 51
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                5               109 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                51 
$`1Q LOSS MUTATED`
TCGA-D3-A3CC TCGA-DA-A1I2 TCGA-DA-A1I8 TCGA-EE-A20H TCGA-EE-A29X 
       45.70        13.68        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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2.86         3.88        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
       39.19         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-EB-A1NK 
        6.64        19.36         7.00        17.56        14.83         0.53 
TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF 
        0.43         1.35         1.28         1.18         0.30         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X 
        0.53         0.26         0.10         0.20         0.39        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-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         6.48         2.43        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-A2OS 
       28.64        42.84        78.44         6.58         1.71        12.10 
TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 
       10.09         5.95        72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
       15.35        24.85        15.35        31.33        84.72        10.09 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D 
       16.21        15.39         5.59        12.16        24.00        14.70 
TCGA-IH-A3EA 
       12.59 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             8.09              0.10 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            45.70             98.76 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            13.68             10.26 
[1] "8.1 - 45.7 (13.7)" "0.1 - 98.8 (10.3)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D40V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1Q LOSS MUTATED                    1             1
  1Q LOSS WILD-TYPE                 26            25
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1Q LOSS MUTATED                                                                                          3
  1Q LOSS WILD-TYPE                                                                                       34
                   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                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         1Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      26
  PRIMARY TUMOR                                                                                           25
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                34
  REGIONAL LYMPH NODE                                                                                    110
D40V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      4    3
  1Q LOSS WILD-TYPE   72  123
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               4                72
  MALE                 3               123
D40V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1    6
  1Q LOSS WILD-TYPE    2  193
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                1                 2
  YES               6               193
                   vv
clus                 M0  M1 M1A M1B M1C
  1Q LOSS MUTATED     6   0   0   0   0
  1Q LOSS WILD-TYPE 170   2   2   2   3
D40V6, multiclass
                   vv
clus                 N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  1Q LOSS MUTATED     4   0   0   0   0   0   2   0   1   0
  1Q LOSS WILD-TYPE 106   2   8  17   1   5  12   6  18   5
D40V7, multiclass
D40V8, 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         1
  1Q LOSS WILD-TYPE           4      16       10       14       20         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1Q LOSS MUTATED           0         1         0          0          0
  1Q LOSS WILD-TYPE        10        22         9          7         21
                   vv
clus                STAGE IIIC STAGE IV
  1Q LOSS MUTATED            2        0
  1Q LOSS WILD-TYPE         25        7
D40V9, multiclass

Clustering(41) Variable = 2p loss mutation analysis
D41V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    6  4
  2P LOSS WILD-TYPE 53 51
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               104 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4                51 
$`2P LOSS MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z3 TCGA-DA-A1I2 TCGA-EB-A24C TCGA-EB-A24D 
       15.25        24.00         2.86        13.68         0.43         1.35 
TCGA-EE-A20B TCGA-EE-A20F TCGA-GN-A264 TCGA-GN-A26D 
       36.07         5.13        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-D9-A3Z4 
       45.70        13.32         9.30         5.39         4.01         3.88 
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-EB-A1NK TCGA-EB-A3HV 
       19.36         7.00        17.56        14.83         0.53         1.28 
TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B 
        1.18         0.30         0.13         0.53         0.26         0.10 
TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        0.20         0.39        11.57         6.31         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
       12.20         4.27         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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A 
        6.58         1.71        12.10        10.09         5.95        72.16 
TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC 
       24.00         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-A263 
        0.20         1.02         0.13        15.35        24.85        15.35 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A 
       84.72        10.09        16.21        15.39         5.59        12.16 
TCGA-GN-A26C TCGA-IH-A3EA 
       24.00        12.59 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.43              0.10 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            36.07             98.76 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           14.190            10.175 
[1] "0.4 - 36.1 (14.2)" "0.1 - 98.8 (10.2)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D41V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2P LOSS MUTATED                    2             2
  2P LOSS WILD-TYPE                 25            24
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2P LOSS MUTATED                                                                                          3
  2P LOSS WILD-TYPE                                                                                       34
                   vv
clus                REGIONAL LYMPH NODE
  2P LOSS MUTATED                    12
  2P LOSS WILD-TYPE                 100
D41V3, multiclass
                                                                                          clus
vv                                                                                         2P LOSS MUTATED
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                   12
                                                                                          clus
vv                                                                                         2P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      25
  PRIMARY TUMOR                                                                                           24
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                34
  REGIONAL LYMPH NODE                                                                                    100
D41V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      7   12
  2P LOSS WILD-TYPE   69  114
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               7                69
  MALE                12               114
D41V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   18
  2P LOSS WILD-TYPE    2  181
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                1                 2
  YES              18               181
                   vv
clus                 M0  M1 M1A M1B M1C
  2P LOSS MUTATED    15   0   0   0   0
  2P LOSS WILD-TYPE 161   2   2   2   3
D41V6, multiclass
                   vv
clus                 N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  2P LOSS MUTATED    10   0   0   1   0   1   3   0   1   1
  2P LOSS WILD-TYPE 100   2   8  16   1   4  11   6  18   4
D41V7, multiclass
D41V8, 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       13       15         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  2P LOSS MUTATED           1         2         0          0          3
  2P LOSS WILD-TYPE         9        21         9          7         18
                   vv
clus                STAGE IIIC STAGE IV
  2P LOSS MUTATED            2        0
  2P LOSS WILD-TYPE         25        7
D41V9, multiclass

Clustering(42) Variable = 2q loss mutation analysis
D42V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    5  3
  2Q LOSS WILD-TYPE 54 52
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                8               106 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                52 
$`2Q LOSS MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-EB-A24C TCGA-EB-A24D TCGA-EE-A20B TCGA-EE-A20F 
       15.25        24.00         0.43         1.35        36.07         5.13 
TCGA-EE-A29D TCGA-GN-A26D 
       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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        3.88        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-EB-A1NK TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 
        0.53         1.28         1.18         0.30         0.13         0.53 
TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z 
        0.26         0.10         0.20         0.39        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A29A 
        1.12         1.35        12.20         4.27         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-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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN 
       78.44         6.58         1.71        12.10        10.09         5.95 
TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
       72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       15.35        31.33        84.72        10.09        16.21        15.39 
TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-IH-A3EA 
        5.59        12.16        24.00        12.59 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.43              0.10 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            36.07             98.76 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           12.925            10.175 
[1] "0.4 - 36.1 (12.9)" "0.1 - 98.8 (10.2)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "2Q LOSS MUTATED"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D42V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2Q LOSS MUTATED                    1             2
  2Q LOSS WILD-TYPE                 26            24
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2Q LOSS MUTATED                                                                                          3
  2Q LOSS WILD-TYPE                                                                                       34
                   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                                                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                   11
                                                                                          clus
vv                                                                                         2Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      26
  PRIMARY TUMOR                                                                                           24
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                34
  REGIONAL LYMPH NODE                                                                                    101
D42V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7   10
  2Q LOSS WILD-TYPE   69  116
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               7                69
  MALE                10               116
D42V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1   16
  2Q LOSS WILD-TYPE    2  183
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                1                 2
  YES              16               183
                   vv
clus                 M0  M1 M1A M1B M1C
  2Q LOSS MUTATED    13   0   0   1   0
  2Q LOSS WILD-TYPE 163   2   2   1   3
D42V6, multiclass
                   vv
clus                 N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  2Q LOSS MUTATED    10   0   0   1   0   0   2   0   2   1
  2Q LOSS WILD-TYPE 100   2   8  16   1   5  12   6  17   4
D42V7, multiclass
D42V8, 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       13       15         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  2Q LOSS MUTATED           1         2         0          0          1
  2Q LOSS WILD-TYPE         9        21         9          7         20
                   vv
clus                STAGE IIIC STAGE IV
  2Q LOSS MUTATED            2        0
  2Q LOSS WILD-TYPE         25        7
D42V9, multiclass

Clustering(43) Variable = 3p loss mutation analysis
D43V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    4  4
  3P LOSS WILD-TYPE 55 51
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                8               106 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                51 
$`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-EB-A24C TCGA-GN-A262 
        0.43        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-D9-A3Z4 TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 
        3.88        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-EB-A1NK TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
       17.56        14.83         0.53         1.35         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y 
        0.30         0.13         0.53         0.26         0.10         0.20 
TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.39        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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN 
       78.44         6.58         1.71        12.10        10.09         5.95 
TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
       72.16        24.00         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-A263 
        6.41         0.20         1.02         0.13        15.35        15.35 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 
       31.33        84.72        10.09        16.21        15.39         5.59 
TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       12.16        24.00        14.70        12.59 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.43              0.10 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            48.79             98.76 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            28.70             10.06 
[1] "0.4 - 48.8 (28.7)" "0.1 - 98.8 (10.1)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D43V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3P LOSS MUTATED                    1             1
  3P LOSS WILD-TYPE                 26            25
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3P LOSS MUTATED                                                                                          5
  3P LOSS WILD-TYPE                                                                                       32
                   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                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                    6
                                                                                          clus
vv                                                                                         3P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      26
  PRIMARY TUMOR                                                                                           25
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                32
  REGIONAL LYMPH NODE                                                                                    106
D43V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5    8
  3P LOSS WILD-TYPE   71  118
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               5                71
  MALE                 8               118
D43V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0   13
  3P LOSS WILD-TYPE    3  186
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                0                 3
  YES              13               186
                   vv
clus                 M0  M1 M1A M1B M1C
  3P LOSS MUTATED    11   0   0   0   0
  3P LOSS WILD-TYPE 165   2   2   2   3
D43V6, 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   1
  3P LOSS WILD-TYPE 105   2   8  16   1   5  11   5  19   4
D43V7, multiclass
D43V8, 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       14       20         9
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  3P LOSS MUTATED           0         1         1          0          3
  3P LOSS WILD-TYPE        10        22         8          7         18
                   vv
clus                STAGE IIIC STAGE IV
  3P LOSS MUTATED            1        0
  3P LOSS WILD-TYPE         26        7
D43V9, multiclass

Clustering(44) Variable = 3q loss mutation analysis
D44V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    5  5
  3Q LOSS WILD-TYPE 54 50
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               104 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5                50 
$`3Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-EB-A24C 
       32.55        48.79        35.80        13.68        36.69         0.43 
TCGA-EE-A29H TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 
        4.41        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-D9-A3Z4 TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
        2.86         3.88        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-EB-A1NK TCGA-EB-A24D TCGA-EB-A3HV 
        7.00        17.56        14.83         0.53         1.35         1.28 
TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B 
        1.18         0.30         0.13         0.53         0.26         0.10 
TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        0.20         0.39        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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN 
       78.44         6.58         1.71        12.10        10.09         5.95 
TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
       72.16        24.00         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-A263 
        6.41         0.20         1.02         0.13        15.35        15.35 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C 
       84.72        10.09        16.21         5.59        12.16        24.00 
TCGA-GN-A26D TCGA-IH-A3EA 
       14.70        12.59 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.43              0.10 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            48.79             98.76 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            28.09             10.06 
[1] "0.4 - 48.8 (28.1)" "0.1 - 98.8 (10.1)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D44V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3Q LOSS MUTATED                    0             1
  3Q LOSS WILD-TYPE                 27            25
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3Q LOSS MUTATED                                                                                          4
  3Q LOSS WILD-TYPE                                                                                       33
                   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                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                    8
                                                                                          clus
vv                                                                                         3Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      27
  PRIMARY TUMOR                                                                                           25
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                33
  REGIONAL LYMPH NODE                                                                                    104
D44V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      6    7
  3Q LOSS WILD-TYPE   70  119
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               6                70
  MALE                 7               119
D44V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   13
  3Q LOSS WILD-TYPE    3  186
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                0                 3
  YES              13               186
                   vv
clus                 M0  M1 M1A M1B M1C
  3Q LOSS MUTATED    11   0   0   0   0
  3Q LOSS WILD-TYPE 165   2   2   2   3
D44V6, 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   1
  3Q LOSS WILD-TYPE 105   2   8  16   1   5  11   5  19   4
D44V7, multiclass
D44V8, 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       15       20         9
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  3Q LOSS MUTATED           1         1         1          0          3
  3Q LOSS WILD-TYPE         9        22         8          7         18
                   vv
clus                STAGE IIIC STAGE IV
  3Q LOSS MUTATED            1        0
  3Q LOSS WILD-TYPE         26        7
D44V9, multiclass

Clustering(45) Variable = 4p loss mutation analysis
D45V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    6  5
  4P LOSS WILD-TYPE 53 50
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               11               103 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5                50 
$`4P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-EB-A3HV 
       16.47        10.26        45.70         2.86        35.80         1.28 
TCGA-EB-A3XC TCGA-EE-A29C TCGA-ER-A19D TCGA-FW-A3TU TCGA-GN-A266 
        0.30        37.97         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-D9-A3Z4 TCGA-DA-A1HV 
       24.00         9.30         5.39         4.01         3.88        48.79 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D 
        7.00        17.56        14.83         0.53         0.43         1.35 
TCGA-EB-A3XB TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y 
        1.18         0.13         0.53         0.26         0.10         0.20 
TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.39        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-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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN 
        1.71        12.10        10.09         5.95        72.16        24.00 
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-A263 TCGA-GN-A264 TCGA-GN-A265 
        1.02        15.35        24.85        15.35        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D 
       16.21        15.39         5.59        12.16        24.00        14.70 
TCGA-IH-A3EA 
       12.59 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.13              0.10 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            45.70             98.76 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            10.09             11.11 
[1] "0.1 - 45.7 (10.1)" "0.1 - 98.8 (11.1)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D45V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4P LOSS MUTATED                    4             3
  4P LOSS WILD-TYPE                 23            23
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4P LOSS MUTATED                                                                                          6
  4P LOSS WILD-TYPE                                                                                       31
                   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                                                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               6
  REGIONAL LYMPH NODE                                                                                    9
                                                                                          clus
vv                                                                                         4P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      23
  PRIMARY TUMOR                                                                                           23
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                31
  REGIONAL LYMPH NODE                                                                                    103
D45V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     12   10
  4P LOSS WILD-TYPE   64  116
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              12                64
  MALE                10               116
D45V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      0   22
  4P LOSS WILD-TYPE    3  177
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                0                 3
  YES              22               177
                   vv
clus                 M0  M1 M1A M1B M1C
  4P LOSS MUTATED    18   0   0   1   0
  4P LOSS WILD-TYPE 158   2   2   1   3
D45V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  4P LOSS MUTATED   13  0   0   2  0   1   0   1  2  0
  4P LOSS WILD-TYPE 97  2   8  15  1   4  14   5 17  5
D45V7, multiclass
D45V8, 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       13       18         9
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4P LOSS MUTATED           1         5         0          1          3
  4P LOSS WILD-TYPE         9        18         9          6         18
                   vv
clus                STAGE IIIC STAGE IV
  4P LOSS MUTATED            1        0
  4P LOSS WILD-TYPE         26        7
D45V9, multiclass

Clustering(46) Variable = 4q loss mutation analysis
D46V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    8  6
  4Q LOSS WILD-TYPE 51 49
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               14               100 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                6                49 
$`4Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3CC TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-EB-A24C 
       16.47        28.08        45.70         2.86        35.80         0.43 
TCGA-EB-A3HV TCGA-EB-A3XC TCGA-EB-A41B TCGA-EE-A181 TCGA-EE-A29C TCGA-ER-A19D 
        1.28         0.30         0.10         1.12        37.97         3.52 
TCGA-FW-A3TU TCGA-GN-A266 
        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-D9-A3Z4 TCGA-DA-A1HV 
       24.00         9.30         5.39         4.01         3.88        48.79 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        10.03        39.19        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-EB-A1NK TCGA-EB-A24D TCGA-EB-A3XB 
        7.00        17.56        14.83         0.53         1.35         1.18 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X 
        0.13         0.53         0.26         0.20         0.39        11.57 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        6.31         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-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        9.67         8.94        11.11         4.18        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A2OS TCGA-FR-A3R1 
       42.84        78.44         6.58         1.71        12.10        10.09 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 
        5.95        72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 
       15.35        31.33        84.72        16.21        15.39         5.59 
TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       12.16        24.00        14.70        12.59 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.10              0.13 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            45.70             98.76 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             3.19             11.13 
[1] "0.1 - 45.7 (3.2)"  "0.1 - 98.8 (11.1)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D46V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4Q LOSS MUTATED                    2             5
  4Q LOSS WILD-TYPE                 25            21
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4Q LOSS MUTATED                                                                                          6
  4Q LOSS WILD-TYPE                                                                                       31
                   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                                                                                          5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               6
  REGIONAL LYMPH NODE                                                                                   10
                                                                                          clus
vv                                                                                         4Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      25
  PRIMARY TUMOR                                                                                           21
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                31
  REGIONAL LYMPH NODE                                                                                    102
D46V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     12   11
  4Q LOSS WILD-TYPE   64  115
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              12                64
  MALE                11               115
D46V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      0   23
  4Q LOSS WILD-TYPE    3  176
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                0                 3
  YES              23               176
                   vv
clus                 M0  M1 M1A M1B M1C
  4Q LOSS MUTATED    18   0   0   2   0
  4Q LOSS WILD-TYPE 158   2   2   0   3
D46V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  4Q LOSS MUTATED   13  0   0   2  0   1   0   0  3  1
  4Q LOSS WILD-TYPE 97  2   8  15  1   4  14   6 16  4
D46V7, multiclass
D46V8, 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       13       17         9
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4Q LOSS MUTATED           0         7         0          1          2
  4Q LOSS WILD-TYPE        10        16         9          6         19
                   vv
clus                STAGE IIIC STAGE IV
  4Q LOSS MUTATED            1        1
  4Q LOSS WILD-TYPE         26        6
D46V9, multiclass

Clustering(47) Variable = 5p loss mutation analysis
D47V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    7  6
  5P LOSS WILD-TYPE 52 49
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               13               101 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6                49 
$`5P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D9-A3Z4 TCGA-EB-A3XC TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29C 
       16.47         3.88         0.30        11.57         4.27        37.97 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2A2 TCGA-FS-A4F2 TCGA-GN-A262 TCGA-GN-A266 
       38.63        27.12        23.90         3.22        24.85        10.09 
TCGA-GN-A268 
       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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XF 
        0.53         0.43         1.35         1.28         1.18         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17Z 
        0.53         0.26         0.10         0.20         0.39         6.31 
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-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
        7.96        11.15         4.41         1.08         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-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F 
       11.31        25.28         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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN 
        1.71        12.10        10.09         5.95        72.16        24.00 
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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        0.13        15.35        15.35        31.33        84.72        16.21 
TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
        5.59        12.16        24.00        14.70        12.59 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              0.3               0.1 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            38.63             98.76 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            15.39             10.09 
[1] "0.3 - 38.6 (15.4)" "0.1 - 98.8 (10.1)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D47V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5P LOSS MUTATED                    3             3
  5P LOSS WILD-TYPE                 24            23
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5P LOSS MUTATED                                                                                          5
  5P LOSS WILD-TYPE                                                                                       32
                   vv
clus                REGIONAL LYMPH NODE
  5P LOSS MUTATED                    14
  5P LOSS WILD-TYPE                  98
D47V3, multiclass
                                                                                          clus
vv                                                                                         5P LOSS MUTATED
  DISTANT METASTASIS                                                                                     3
  PRIMARY TUMOR                                                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                   14
                                                                                          clus
vv                                                                                         5P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      24
  PRIMARY TUMOR                                                                                           23
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                32
  REGIONAL LYMPH NODE                                                                                     98
D47V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      9   16
  5P LOSS WILD-TYPE   67  110
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               9                67
  MALE                16               110
D47V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1   24
  5P LOSS WILD-TYPE    2  175
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                1                 2
  YES              24               175
                   vv
clus                 M0  M1 M1A M1B M1C
  5P LOSS MUTATED    20   0   0   0   0
  5P LOSS WILD-TYPE 156   2   2   2   3
D47V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  5P LOSS MUTATED   11  0   0   3  0   1   2   1  3  0
  5P LOSS WILD-TYPE 99  2   8  14  1   4  12   5 16  5
D47V7, multiclass
D47V8, 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         0
  5P LOSS WILD-TYPE           4      15        8       13       19         9
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5P LOSS MUTATED           2         2         2          1          2
  5P LOSS WILD-TYPE         8        21         7          6         19
                   vv
clus                STAGE IIIC STAGE IV
  5P LOSS MUTATED            4        0
  5P LOSS WILD-TYPE         23        7
D47V9, multiclass

Clustering(48) Variable = 5q loss mutation analysis
D48V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   10 13
  5Q LOSS WILD-TYPE 49 42
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               23                91 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               13                42 
$`5Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z4 
       28.08         6.35        15.25        24.00         4.01         3.88 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EB-A3XC TCGA-EE-A17X 
       35.80        10.03        44.52        36.69         0.30        11.57 
TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29V 
        4.27         8.81        37.97        38.63        27.12         2.43 
TCGA-EE-A2A2 TCGA-GN-A262 TCGA-GN-A263 TCGA-GN-A266 TCGA-GN-A268 
       23.90        24.85        15.35        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-EB-A1NK TCGA-EB-A24C 
       19.36         7.00        17.56        14.83         0.53         0.43 
TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A 
        1.35         1.28         1.18         0.13         0.53         0.26 
TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        0.10         0.20         0.39         6.31         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29H 
       12.20        36.07         5.13         7.96        11.15         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08         9.47        12.03         8.12         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
        6.48         8.09        11.31        25.28         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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN 
       78.44         6.58         1.71        12.10        10.09         5.95 
TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
       72.16        24.00         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-A267 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D 
       84.72        16.21         5.59        12.16        24.00        14.70 
TCGA-IH-A3EA 
       12.59 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              0.3               0.1 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            44.52             98.76 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            15.35              9.99 
[1] "0.3 - 44.5 (15.3)" "0.1 - 98.8 (10.0)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5Q LOSS MUTATED                    7             4
  5Q LOSS WILD-TYPE                 20            22
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5Q LOSS MUTATED                                                                                          7
  5Q LOSS WILD-TYPE                                                                                       30
                   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                                                                                          4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   23
                                                                                          clus
vv                                                                                         5Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      20
  PRIMARY TUMOR                                                                                           22
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                30
  REGIONAL LYMPH NODE                                                                                     89
D48V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     13   28
  5Q LOSS WILD-TYPE   63   98
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              13                63
  MALE                28                98
D48V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1   40
  5Q LOSS WILD-TYPE    2  159
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                1                 2
  YES              40               159
                   vv
clus                 M0  M1 M1A M1B M1C
  5Q LOSS MUTATED    32   0   1   1   2
  5Q LOSS WILD-TYPE 144   2   1   1   1
D48V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  5Q LOSS MUTATED   18  0   0   5  0   1   4   1  7  1
  5Q LOSS WILD-TYPE 92  2   8  12  1   4  10   5 12  4
D48V7, multiclass
D48V8, 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       12       17         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5Q LOSS MUTATED           1         1         2          1          4
  5Q LOSS WILD-TYPE         9        22         7          6         17
                   vv
clus                STAGE IIIC STAGE IV
  5Q LOSS MUTATED            8        3
  5Q LOSS WILD-TYPE         19        4
D48V9, multiclass

Clustering(49) Variable = 6p loss mutation analysis
D49V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED    3  6
  6P LOSS WILD-TYPE 56 49
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                9               105 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                49 
$`6P LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-EE-A29D TCGA-EE-A29M 
       22.55        10.26        51.12        25.15        11.15        27.12 
TCGA-EE-A29Q TCGA-EE-A29X TCGA-EE-A2A0 
        8.12         8.09        11.31 

$`6P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 
       16.47        32.55        70.16        98.76        28.08         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
        3.88        48.79        35.80        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
        9.99        44.52        36.69         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A1NK TCGA-EB-A24C 
       19.36         7.00        17.56        14.83         0.53         0.43 
TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 
        1.35         1.28         1.18         0.30         0.13         0.53 
TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z 
        0.26         0.10         0.20         0.39        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-A29E TCGA-EE-A29H TCGA-EE-A29L 
        8.81         7.96        37.97        38.63         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
        9.47        12.03         8.84         9.99         6.48         2.43 
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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN 
        1.71        12.10        10.09         5.95        72.16        24.00 
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-A263 TCGA-GN-A264 
        1.02         0.13        15.35        24.85        15.35        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A 
       84.72        10.09        16.21        15.39         5.59        12.16 
TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       24.00        14.70        12.59 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             8.09              0.10 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            51.12             98.76 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            11.31             10.09 
[1] "8.1 - 51.1 (11.3)" "0.1 - 98.8 (10.1)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D49V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6P LOSS MUTATED                    4             1
  6P LOSS WILD-TYPE                 23            25
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6P LOSS MUTATED                                                                                          3
  6P LOSS WILD-TYPE                                                                                       34
                   vv
clus                REGIONAL LYMPH NODE
  6P LOSS MUTATED                     8
  6P LOSS WILD-TYPE                 104
D49V3, multiclass
                                                                                          clus
vv                                                                                         6P LOSS MUTATED
  DISTANT METASTASIS                                                                                     4
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    8
                                                                                          clus
vv                                                                                         6P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      23
  PRIMARY TUMOR                                                                                           25
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                34
  REGIONAL LYMPH NODE                                                                                    104
D49V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      7    9
  6P LOSS WILD-TYPE   69  117
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               7                69
  MALE                 9               117
D49V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   16
  6P LOSS WILD-TYPE    3  183
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                0                 3
  YES              16               183
                   vv
clus                 M0  M1 M1A M1B M1C
  6P LOSS MUTATED    15   0   0   0   0
  6P LOSS WILD-TYPE 161   2   2   2   3
D49V6, multiclass
                   vv
clus                 N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  6P LOSS MUTATED    10   0   0   2   0   1   0   0   2   0
  6P LOSS WILD-TYPE 100   2   8  15   1   4  14   6  17   5
D49V7, multiclass
D49V8, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6P LOSS MUTATED             1       1        0        3        2         1
  6P LOSS WILD-TYPE           3      16       10       12       18         8
                   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        23         8          7         20
                   vv
clus                STAGE IIIC STAGE IV
  6P LOSS MUTATED            3        0
  6P LOSS WILD-TYPE         24        7
D49V9, multiclass

Clustering(50) Variable = 6q loss mutation analysis
D50V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   24 22
  6Q LOSS WILD-TYPE 35 33
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               46                68 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22                33 
$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 
        2.86         3.88        48.79        51.12        39.19         9.99 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EB-A24D TCGA-EB-A3XB 
       36.69        25.15         6.64        17.56         1.35         1.18 
TCGA-EB-A3XC TCGA-EB-A3Y6 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H 
        0.30         0.53         1.35         4.27        36.07         8.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29Q 
        7.96        37.97        11.15         4.41        27.12         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-A3PL TCGA-FS-A1ZR 
        9.67         8.94         3.52        11.11         1.71         8.81 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A268 TCGA-GN-A26A 
        0.20         1.02        15.39        12.16 

$`6Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       70.16        98.76        28.08         8.38        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV 
        6.35        45.70        13.32        24.00         9.30         5.39 
TCGA-D9-A3Z1 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-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-EB-A1NK TCGA-EB-A24C 
       22.36        19.36         7.00        14.83         0.53         0.43 
TCGA-EB-A3HV TCGA-EB-A3XF TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z 
        1.28         0.13         0.26         0.10         0.20         0.39 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29E 
       11.57         6.31         1.12        12.20         5.13        38.63 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-ER-A19J 
        1.08         9.47        12.03         8.84         6.48         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A2OS 
       12.99        28.64        42.84        78.44         6.58        12.10 
TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A4F0 TCGA-FS-A4F2 
       10.09         5.95        72.16        24.00        53.82         3.22 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A263 
       10.78         6.41         0.13        15.35        24.85        15.35 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A269 TCGA-GN-A26C 
       31.33        84.72        10.09        16.21         5.59        24.00 
TCGA-GN-A26D TCGA-IH-A3EA 
       14.70        12.59 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              0.2               0.1 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            51.12             98.76 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             9.99             11.49 
[1] "0.2 - 51.1 (10.0)" "0.1 - 98.8 (11.5)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"6Q LOSS WILD-TYPE" "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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"6Q LOSS WILD-TYPE" "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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D50V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6Q LOSS MUTATED                   14             7
  6Q LOSS WILD-TYPE                 13            19
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6Q LOSS MUTATED                                                                                         17
  6Q LOSS WILD-TYPE                                                                                       20
                   vv
clus                REGIONAL LYMPH NODE
  6Q LOSS MUTATED                    36
  6Q LOSS WILD-TYPE                  76
D50V3, multiclass
                                                                                          clus
vv                                                                                         6Q LOSS MUTATED
  DISTANT METASTASIS                                                                                    14
  PRIMARY TUMOR                                                                                          7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              17
  REGIONAL LYMPH NODE                                                                                   36
                                                                                          clus
vv                                                                                         6Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      13
  PRIMARY TUMOR                                                                                           19
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                20
  REGIONAL LYMPH NODE                                                                                     76
D50V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     29   45
  6Q LOSS WILD-TYPE   47   81
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              29                47
  MALE                45                81
D50V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   74
  6Q LOSS WILD-TYPE    3  125
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                0                 3
  YES              74               125
                   vv
clus                 M0  M1 M1A M1B M1C
  6Q LOSS MUTATED    66   1   1   1   1
  6Q LOSS WILD-TYPE 110   1   1   1   2
D50V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  6Q LOSS MUTATED   40  0   3   7  1   1   5   3  8  2
  6Q LOSS WILD-TYPE 70  2   5  10  0   4   9   3 11  3
D50V7, multiclass
D50V8, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6Q LOSS MUTATED             3       4        5        8        7         2
  6Q LOSS WILD-TYPE           1      13        5        7       13         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6Q LOSS MUTATED           4         5         3          2         10
  6Q LOSS WILD-TYPE         6        18         6          5         11
                   vv
clus                STAGE IIIC STAGE IV
  6Q LOSS MUTATED           11        3
  6Q LOSS WILD-TYPE         16        4
D50V9, multiclass

Clustering(51) Variable = 7p loss mutation analysis
D51V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    0  2
  7P LOSS WILD-TYPE 59 53
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2               112 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2                53 
$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2.86         3.88        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
       14.83         0.53         0.43         1.35         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y 
        0.30         0.13         0.53         0.26         0.10         0.20 
TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.39        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-A2A6 TCGA-ER-A19D 
        8.09        11.31        25.28        23.90         8.94         3.52 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A 
        6.58         1.71        12.10        10.09         5.95        72.16 
TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC 
       24.00         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-A263 
        0.20         1.02         0.13        15.35        24.85        15.35 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 
       31.33        84.72        10.09        16.21        15.39         5.59 
TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       12.16        24.00        14.70        12.59 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             9.67              0.10 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            13.32             98.76 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           11.495            10.520 
[1] "9.7 - 13.3 (11.5)" "0.1 - 98.8 (10.5)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2               112 
       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-D9-A3Z4 
"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-EB-A1NK        TCGA-EB-A24C        TCGA-EB-A24D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC        TCGA-EB-A3XF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B        TCGA-EB-A42Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EB-A42Z        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-A2A6        TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19J 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N        TCGA-ER-A1A1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A2OS        TCGA-FR-A3R1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FR-A3YN        TCGA-FR-A44A        TCGA-FS-A1ZN        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-A263        TCGA-GN-A264        TCGA-GN-A265 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A269 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26C        TCGA-GN-A26D        TCGA-IH-A3EA 
"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                 26            26
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7P LOSS MUTATED                                                                                          1
  7P LOSS WILD-TYPE                                                                                       36
                   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                                                                                      26
  PRIMARY TUMOR                                                                                           26
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                36
  REGIONAL LYMPH NODE                                                                                    111
D51V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    1
  7P LOSS WILD-TYPE   74  125
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               2                74
  MALE                 1               125
D51V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    3
  7P LOSS WILD-TYPE    3  196
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                0                 3
  YES               3               196
                   vv
clus                 M0  M1 M1A M1B M1C
  7P LOSS MUTATED     3   0   0   0   0
  7P LOSS WILD-TYPE 173   2   2   2   3
D51V6, 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 108   2   8  16   1   5  14   6  19   5
D51V7, multiclass
D51V8, 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       14       20         9
                   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        22         8          7         21
                   vv
clus                STAGE IIIC STAGE IV
  7P LOSS MUTATED            0        0
  7P LOSS WILD-TYPE         27        7
D51V9, multiclass

Clustering(52) Variable = 7q loss mutation analysis
D52V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    0  2
  7Q LOSS WILD-TYPE 59 53
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2               112 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2                53 
$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2.86         3.88        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
       14.83         0.53         0.43         1.35         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y 
        0.30         0.13         0.53         0.26         0.10         0.20 
TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.39        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-A2A6 TCGA-ER-A19D 
        8.09        11.31        25.28        23.90         8.94         3.52 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A 
        6.58         1.71        12.10        10.09         5.95        72.16 
TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC 
       24.00         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-A263 
        0.20         1.02         0.13        15.35        24.85        15.35 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 
       31.33        84.72        10.09        16.21        15.39         5.59 
TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       12.16        24.00        14.70        12.59 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             9.67              0.10 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            13.32             98.76 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           11.495            10.520 
[1] "9.7 - 13.3 (11.5)" "0.1 - 98.8 (10.5)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2               112 
       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-D9-A3Z4 
"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-EB-A1NK        TCGA-EB-A24C        TCGA-EB-A24D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC        TCGA-EB-A3XF 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B        TCGA-EB-A42Y 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EB-A42Z        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-A2A6        TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19J 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N        TCGA-ER-A1A1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A2OS        TCGA-FR-A3R1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FR-A3YN        TCGA-FR-A44A        TCGA-FS-A1ZN        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-A263        TCGA-GN-A264        TCGA-GN-A265 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A269 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26C        TCGA-GN-A26D        TCGA-IH-A3EA 
"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                 26            26
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7Q LOSS MUTATED                                                                                          1
  7Q LOSS WILD-TYPE                                                                                       36
                   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                                                                                      26
  PRIMARY TUMOR                                                                                           26
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                36
  REGIONAL LYMPH NODE                                                                                    111
D52V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    1
  7Q LOSS WILD-TYPE   74  125
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               2                74
  MALE                 1               125
D52V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    3
  7Q LOSS WILD-TYPE    3  196
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                0                 3
  YES               3               196
                   vv
clus                 M0  M1 M1A M1B M1C
  7Q LOSS MUTATED     3   0   0   0   0
  7Q LOSS WILD-TYPE 173   2   2   2   3
D52V6, 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 108   2   8  16   1   5  14   6  19   5
D52V7, multiclass
D52V8, 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       14       20         9
                   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        22         8          7         21
                   vv
clus                STAGE IIIC STAGE IV
  7Q LOSS MUTATED            0        0
  7Q LOSS WILD-TYPE         27        7
D52V9, multiclass

Clustering(53) Variable = 8p loss mutation analysis
D53V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    8  7
  8P LOSS WILD-TYPE 51 48
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               15                99 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                7                48 
$`8P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A3XC 
       16.47        15.25         9.30         0.53         0.43         0.30 
TCGA-EB-A41B TCGA-EB-A42Z TCGA-EE-A183 TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29V 
        0.10         0.39        12.20        37.97         4.41         2.43 
TCGA-EE-A2A5 TCGA-GN-A264 TCGA-IH-A3EA 
        9.67        31.33        12.59 

$`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-D9-A3Z4 
       13.32        24.00         5.39         4.01         2.86         3.88 
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-EB-A24D 
        6.64        19.36         7.00        17.56        14.83         1.35 
TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A42Y 
        1.28         1.18         0.13         0.53         0.26         0.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B 
       11.57         6.31         1.12         1.35         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L 
        5.13         8.81         7.96        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-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        6.48         8.09        11.31        25.28        23.90         8.94 
TCGA-ER-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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN 
       78.44         6.58         1.71        12.10        10.09         5.95 
TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
       72.16        24.00         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-A263 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 
       15.35        84.72        10.09        16.21        15.39         5.59 
TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D 
       12.16        24.00        14.70 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.10              0.13 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            37.97             98.76 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             9.30             11.11 
[1] "0.1 - 38.0 (9.3)"  "0.1 - 98.8 (11.1)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
[1] "hr=" "1.4"
D53V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8P LOSS MUTATED                    6             6
  8P LOSS WILD-TYPE                 21            20
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8P LOSS MUTATED                                                                                          2
  8P LOSS WILD-TYPE                                                                                       35
                   vv
clus                REGIONAL LYMPH NODE
  8P LOSS MUTATED                    13
  8P LOSS WILD-TYPE                  99
D53V3, multiclass
                                                                                          clus
vv                                                                                         8P LOSS MUTATED
  DISTANT METASTASIS                                                                                     6
  PRIMARY TUMOR                                                                                          6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                   13
                                                                                          clus
vv                                                                                         8P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      21
  PRIMARY TUMOR                                                                                           20
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                35
  REGIONAL LYMPH NODE                                                                                     99
D53V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      8   19
  8P LOSS WILD-TYPE   68  107
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               8                68
  MALE                19               107
D53V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   27
  8P LOSS WILD-TYPE    3  172
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                0                 3
  YES              27               172
                   vv
clus                 M0  M1 M1A M1B M1C
  8P LOSS MUTATED    23   0   0   1   0
  8P LOSS WILD-TYPE 153   2   2   1   3
D53V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  8P LOSS MUTATED   15  0   0   3  0   1   0   2  2  1
  8P LOSS WILD-TYPE 95  2   8  14  1   4  14   4 17  4
D53V7, multiclass
D53V8, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8P LOSS MUTATED             1       3        2        3        1         1
  8P LOSS WILD-TYPE           3      14        8       12       19         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8P LOSS MUTATED           0         5         2          0          1
  8P LOSS WILD-TYPE        10        18         7          7         20
                   vv
clus                STAGE IIIC STAGE IV
  8P LOSS MUTATED            3        0
  8P LOSS WILD-TYPE         24        7
D53V9, multiclass

Clustering(54) Variable = 8q loss mutation analysis
D54V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    3  0
  8Q LOSS WILD-TYPE 56 55
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               111 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                55 
$`8Q LOSS MUTATED`
TCGA-EB-A24C TCGA-EB-A3XC TCGA-EB-A41B 
        0.43         0.30         0.10 

$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        4.01         2.86         3.88        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-EB-A1NK TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
       17.56        14.83         0.53         1.35         1.28         1.18 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X 
        0.13         0.53         0.26         0.20         0.39        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-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-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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN 
        1.71        12.10        10.09         5.95        72.16        24.00 
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-A263 TCGA-GN-A264 
        1.02         0.13        15.35        24.85        15.35        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A 
       84.72        10.09        16.21        15.39         5.59        12.16 
TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       24.00        14.70        12.59 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.10              0.13 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.43             98.76 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.30             11.11 
[1] "0.1 - 0.4 (0.3)"   "0.1 - 98.8 (11.1)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
[1] "hr=" NA   
D54V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8Q LOSS MUTATED                    1             3
  8Q LOSS WILD-TYPE                 26            23
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8Q LOSS MUTATED                                                                                          0
  8Q LOSS WILD-TYPE                                                                                       37
                   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                                                                                          3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         8Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      26
  PRIMARY TUMOR                                                                                           23
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                37
  REGIONAL LYMPH NODE                                                                                    110
D54V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    3
  8Q LOSS WILD-TYPE   73  123
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               3                73
  MALE                 3               123
D54V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    6
  8Q LOSS WILD-TYPE    3  193
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                 3
  YES               6               193
                   vv
clus                 M0  M1 M1A M1B M1C
  8Q LOSS MUTATED     6   0   0   0   0
  8Q LOSS WILD-TYPE 170   2   2   2   3
D54V6, multiclass
                   vv
clus                 N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  8Q LOSS MUTATED     4   0   0   0   0   0   0   1   0   1
  8Q LOSS WILD-TYPE 106   2   8  17   1   5  14   5  19   4
D54V7, multiclass
D54V8, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8Q LOSS MUTATED             0       1        0        0        1         0
  8Q LOSS WILD-TYPE           4      16       10       15       19         9
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8Q LOSS MUTATED           0         3         0          0          1
  8Q LOSS WILD-TYPE        10        20         9          7         20
                   vv
clus                STAGE IIIC STAGE IV
  8Q LOSS MUTATED            0        0
  8Q LOSS WILD-TYPE         27        7
D54V9, multiclass

Clustering(55) Variable = 9p loss mutation analysis
D55V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   33 37
  9P LOSS WILD-TYPE 26 18
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               70                44 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               37                18 
$`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-D9-A3Z4 
        6.35        15.25        24.00         9.30         2.86         3.88 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.79        35.80        51.12        39.19        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EB-A24C TCGA-EB-A24D 
       44.52        25.15         4.93         6.64         0.43         1.35 
TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A 
        1.28         1.18         0.30         0.13         0.53         0.26 
TCGA-EB-A41B TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 
        0.10         0.39        11.57         1.12         1.35         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       36.07         5.13         8.81        37.97        11.15        38.63 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
        1.08         9.47        12.03         8.12         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L 
        8.09        11.31         9.67         3.52        11.11        12.99 
TCGA-ER-A19M TCGA-ER-A3PL TCGA-FR-A2OS TCGA-FR-A3YN TCGA-FS-A1ZR TCGA-FS-A4F0 
       28.64         1.71        12.10         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-A263 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       15.35        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-EB-A1NK TCGA-EB-A42Y 
       19.36         7.00        17.56        14.83         0.53         0.20 
TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A29A TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R 
        6.31        12.20         7.96         4.41        27.12         8.84 
TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A19N 
        6.48        25.28        23.90         8.94         4.18        42.84 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A3R1 TCGA-FR-A44A TCGA-FS-A1ZN TCGA-GN-A261 
       78.44         6.58        10.09        72.16        24.00        15.35 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A269 
       24.85        31.33        84.72        10.09        16.21         5.59 
TCGA-GN-A26C TCGA-IH-A3EA 
       24.00        12.59 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              0.1               0.2 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            70.16             98.76 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            9.570            14.075 
[1] "0.1 - 70.2 (9.6)"  "0.2 - 98.8 (14.1)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D55V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9P LOSS MUTATED                   18            15
  9P LOSS WILD-TYPE                  9            11
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9P LOSS MUTATED                                                                                         27
  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                                                                                         15
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              27
  REGIONAL LYMPH NODE                                                                                   57
                                                                                          clus
vv                                                                                         9P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       9
  PRIMARY TUMOR                                                                                           11
  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     44   73
  9P LOSS WILD-TYPE   32   53
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              44                32
  MALE                73                53
D55V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1  116
  9P LOSS WILD-TYPE    2   83
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                1                 2
  YES             116                83
                   vv
clus                 M0  M1 M1A M1B M1C
  9P LOSS MUTATED   101   1   1   2   3
  9P LOSS WILD-TYPE  75   1   1   0   0
D55V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  9P LOSS MUTATED   68  0   4  12  1   0   6   5 12  2
  9P LOSS WILD-TYPE 42  2   4   5  0   5   8   1  7  3
D55V7, multiclass
D55V8, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9P LOSS MUTATED             4       4        4       10       15         7
  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        14         4          2         12
  9P LOSS WILD-TYPE         3         9         5          5          9
                   vv
clus                STAGE IIIC STAGE IV
  9P LOSS MUTATED           16        6
  9P LOSS WILD-TYPE         11        1
D55V9, multiclass

Clustering(56) Variable = 9q loss mutation analysis
D56V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   20 25
  9Q LOSS WILD-TYPE 39 30
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               45                69 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               25                30 
$`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-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EE-A181 
        6.64         1.18         0.30         0.13         0.53         1.12 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29N 
       36.07         5.13         8.81        11.15         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 
       12.03         8.12         9.99         8.09        11.31        23.90 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19M TCGA-ER-A3PL TCGA-FS-A1ZR TCGA-FS-A4F0 
        3.52        11.11        28.64         1.71         8.81        53.82 
TCGA-FS-A4F2 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A263 
        3.22         6.41         0.20         1.02        24.85        15.35 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       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-D9-A3Z4 TCGA-DA-A1HY 
        9.30         5.39         4.01         2.86         3.88        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       10.03        36.69        22.36        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A41A 
       14.83         0.53         0.43         1.35         1.28         0.26 
TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 
        0.10         0.20         0.39        11.57         6.31         1.35 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       12.20         4.27         7.96        37.97        38.63         4.41 
TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A5 
       27.12         8.84         6.48         2.43        25.28         9.67 
TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
        8.94         4.18        12.99        42.84        78.44         6.58 
TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A4F9 
       12.10        10.09         5.95        72.16        24.00        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 
TCGA-GN-A269 TCGA-GN-A26C TCGA-IH-A3EA 
        5.59        24.00        12.59 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.13              0.10 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            53.82             98.76 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            11.11             10.26 
[1] "0.1 - 53.8 (11.1)" "0.1 - 98.8 (10.3)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D56V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9Q LOSS MUTATED                   14             7
  9Q LOSS WILD-TYPE                 13            19
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9Q LOSS MUTATED                                                                                         20
  9Q LOSS WILD-TYPE                                                                                       17
                   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                                                                                          7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              20
  REGIONAL LYMPH NODE                                                                                   42
                                                                                          clus
vv                                                                                         9Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      13
  PRIMARY TUMOR                                                                                           19
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                17
  REGIONAL LYMPH NODE                                                                                     70
D56V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     38   45
  9Q LOSS WILD-TYPE   38   81
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              38                38
  MALE                45                81
D56V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   82
  9Q LOSS WILD-TYPE    2  117
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                1                 2
  YES              82               117
                   vv
clus                 M0  M1 M1A M1B M1C
  9Q LOSS MUTATED    68   1   1   2   3
  9Q LOSS WILD-TYPE 108   1   1   0   0
D56V6, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  9Q LOSS MUTATED   49  0   4   5  1   1   5   4  7  1
  9Q LOSS WILD-TYPE 61  2   4  12  0   4   9   2 12  4
D56V7, multiclass
D56V8, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9Q LOSS MUTATED             3       2        2        7       11         5
  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         8         3          3          9
  9Q LOSS WILD-TYPE         3        15         6          4         12
                   vv
clus                STAGE IIIC STAGE IV
  9Q LOSS MUTATED            6        6
  9Q LOSS WILD-TYPE         21        1
D56V9, multiclass

Clustering(57) Variable = 10p loss mutation analysis
D57V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   20 28
  10P LOSS WILD-TYPE 39 27
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                48                 66 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                28                 27 
$`10P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2JK TCGA-D3-A3CE 
       16.47        32.55        98.76        28.08         6.35        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 
       24.00         9.30         2.86        35.80        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-EB-A24C 
        9.99        44.52        36.69        25.15         4.93         0.43 
TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A42Y 
        1.35         1.28         1.18         0.30         0.13         0.20 
TCGA-EB-A42Z TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
        0.39         6.31         4.27        36.07         5.13         8.81 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29X TCGA-EE-A2A5 
        4.41         1.08        27.12        12.03         8.09         9.67 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A3PL TCGA-FR-A2OS TCGA-FR-A3YN TCGA-FS-A1ZN 
        3.52        12.99         1.71        12.10         5.95        24.00 
TCGA-FS-A1ZR TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        8.81        31.33        10.09        16.21        15.39        12.16 

$`10P LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       70.16        22.55        10.26         8.38        21.14        11.41 
TCGA-D3-A2JF TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z4 
       30.87        15.25        45.70         5.39         4.01         3.88 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       48.79        51.12        10.03        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A1NK TCGA-EB-A3Y6 TCGA-EB-A41A 
        7.00        17.56        14.83         0.53         0.53         0.26 
TCGA-EB-A41B TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29A 
        0.10        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-ER-A3ET TCGA-FR-A3R1 TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
        6.58        10.09        72.16        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-A263 TCGA-GN-A265 TCGA-GN-A269 TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       15.35        84.72         5.59        24.00        14.70        12.59 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.13               0.10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             98.76              84.72 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              9.83              11.13 
[1] "0.1 - 98.8 (9.8)"  "0.1 - 84.7 (11.1)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        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-D9-A3Z4 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        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-D9-A3Z4 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        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-D9-A3Z4 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D57V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10P LOSS MUTATED                   13            11
  10P LOSS WILD-TYPE                 14            15
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  10P LOSS MUTATED                                                                                         20
  10P LOSS WILD-TYPE                                                                                       17
                    vv
clus                 REGIONAL LYMPH NODE
  10P LOSS MUTATED                    44
  10P LOSS WILD-TYPE                  68
D57V3, multiclass
                                                                                          clus
vv                                                                                         10P LOSS MUTATED
  DISTANT METASTASIS                                                                                     13
  PRIMARY TUMOR                                                                                          11
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               20
  REGIONAL LYMPH NODE                                                                                    44
                                                                                          clus
vv                                                                                         10P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       14
  PRIMARY TUMOR                                                                                            15
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 17
  REGIONAL LYMPH NODE                                                                                      68
D57V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     38   50
  10P LOSS WILD-TYPE   38   76
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               38                 38
  MALE                 50                 76
D57V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   87
  10P LOSS WILD-TYPE    2  112
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 1                  2
  YES               87                112
                    vv
clus                 M0 M1 M1A M1B M1C
  10P LOSS MUTATED   77  0   1   1   2
  10P LOSS WILD-TYPE 99  2   1   1   1
D57V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  10P LOSS MUTATED   49  0   5   6  0   1   8   4  7  2
  10P LOSS WILD-TYPE 61  2   3  11  1   4   6   2 12  3
D57V7, multiclass
D57V8, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  10P LOSS MUTATED             4       7        4        7       10         2
  10P LOSS WILD-TYPE           0      10        6        8       10         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  10P LOSS MUTATED           4        11         4          4          9
  10P LOSS WILD-TYPE         6        12         5          3         12
                    vv
clus                 STAGE IIIC STAGE IV
  10P LOSS MUTATED           11        4
  10P LOSS WILD-TYPE         16        3
D57V9, multiclass

Clustering(58) Variable = 10q loss mutation analysis
D58V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   24 29
  10Q LOSS WILD-TYPE 35 26
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                53                 61 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                29                 26 
$`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-D9-A3Z4 
        6.35        15.25        13.32         9.30         2.86         3.88 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       35.80        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A3F8 TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV 
       25.15         4.93        14.83         0.43         1.35         1.28 
TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A42Z TCGA-EE-A17Z 
        1.18         0.30         0.13         0.53         0.39         6.31 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29H TCGA-EE-A29L 
        4.27        36.07         5.13         8.81         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D 
       27.12        12.03         8.09         9.67         8.94         3.52 
TCGA-ER-A19L TCGA-ER-A3PL TCGA-FR-A2OS TCGA-FR-A3YN TCGA-FS-A1ZN TCGA-FS-A1ZR 
       12.99         1.71        12.10         5.95        24.00         8.81 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       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-EB-A1NK 
       22.36         6.64        19.36         7.00        17.56         0.53 
TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
        0.26         0.10         0.20        11.57         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N 
       12.20         7.96        37.97        11.15        38.63         9.47 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 
        8.12         8.84         9.99         6.48         2.43        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
       25.28        23.90        11.11         4.18        28.64        42.84 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A3R1 TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4F2 
       78.44         6.58        10.09        72.16        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-A263 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26C TCGA-GN-A26D 
       15.35        84.72        15.39         5.59        24.00        14.70 
TCGA-IH-A3EA 
       12.59 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.13               0.10 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             98.76              84.72 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              9.99              11.11 
[1] "0.1 - 98.8 (10.0)" "0.1 - 84.7 (11.1)"
        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-D9-A3Z4 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "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-D9-A3Z4 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "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-D9-A3Z4 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D58V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10Q LOSS MUTATED                   14            13
  10Q LOSS WILD-TYPE                 13            13
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  10Q LOSS MUTATED                                                                                         24
  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                                                                                     14
  PRIMARY TUMOR                                                                                          13
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               24
  REGIONAL LYMPH NODE                                                                                    49
                                                                                          clus
vv                                                                                         10Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       13
  PRIMARY TUMOR                                                                                            13
  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     42   58
  10Q LOSS WILD-TYPE   34   68
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               42                 34
  MALE                 58                 68
D58V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   99
  10Q LOSS WILD-TYPE    2  100
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 1                  2
  YES               99                100
                    vv
clus                 M0 M1 M1A M1B M1C
  10Q LOSS MUTATED   85  0   1   2   2
  10Q LOSS WILD-TYPE 91  2   1   0   1
D58V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  10Q LOSS MUTATED   55  0   5   7  0   2   8   4  8  2
  10Q LOSS WILD-TYPE 55  2   3  10  1   3   6   2 11  3
D58V7, multiclass
D58V8, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  10Q LOSS MUTATED             4       7        6        8       10         4
  10Q LOSS WILD-TYPE           0      10        4        7       10         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  10Q LOSS MUTATED           5        11         5          4         11
  10Q LOSS WILD-TYPE         5        12         4          3         10
                    vv
clus                 STAGE IIIC STAGE IV
  10Q LOSS MUTATED           10        4
  10Q LOSS WILD-TYPE         17        3
D58V9, multiclass

Clustering(59) Variable = 11p loss mutation analysis
D59V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   17 18
  11P LOSS WILD-TYPE 42 37
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                35                 79 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                18                 37 
$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I8 
        3.88        48.79        35.80        39.19        44.52        25.15 
TCGA-EB-A24D TCGA-EB-A3XB TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L 
        1.35         1.18         1.35        37.97        11.15         1.08 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 
       27.12         8.12         8.84         2.43         8.09        23.90 
TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A4F9 
        9.67         3.52        12.99         1.71         5.95        10.78 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A 
        0.20        24.85        31.33        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XC 
       17.56        14.83         0.53         0.43         1.28         0.30 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z 
        0.13         0.53         0.26         0.10         0.20         0.39 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       11.57         6.31         1.12        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N 
        5.13         8.81         7.96        38.63         4.41         9.47 
TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 
       12.03         9.99         6.48        11.31        25.28         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       11.11         4.18        28.64        42.84        78.44         6.58 
TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 
       12.10        10.09        72.16        24.00         8.81        53.82 
TCGA-FS-A4F2 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A263 
        3.22         6.41         1.02         0.13        15.35        15.35 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26C TCGA-GN-A26D 
       84.72        10.09        15.39         5.59        24.00        14.70 
TCGA-IH-A3EA 
       12.59 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               0.2                0.1 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             48.79              98.76 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             10.78              10.09 
[1] "0.2 - 48.8 (10.8)" "0.1 - 98.8 (10.1)"
        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-D9-A3Z4 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "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-D9-A3Z4 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "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-D9-A3Z4 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D59V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11P LOSS MUTATED                    8             6
  11P LOSS WILD-TYPE                 19            20
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11P LOSS MUTATED                                                                                         11
  11P LOSS WILD-TYPE                                                                                       26
                    vv
clus                 REGIONAL LYMPH NODE
  11P LOSS MUTATED                    26
  11P LOSS WILD-TYPE                  86
D59V3, multiclass
                                                                                          clus
vv                                                                                         11P LOSS MUTATED
  DISTANT METASTASIS                                                                                      8
  PRIMARY TUMOR                                                                                           6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               11
  REGIONAL LYMPH NODE                                                                                    26
                                                                                          clus
vv                                                                                         11P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       19
  PRIMARY TUMOR                                                                                            20
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 26
  REGIONAL LYMPH NODE                                                                                      86
D59V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     23   28
  11P LOSS WILD-TYPE   53   98
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               23                 53
  MALE                 28                 98
D59V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   51
  11P LOSS WILD-TYPE    3  148
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 0                  3
  YES               51                148
                    vv
clus                  M0  M1 M1A M1B M1C
  11P LOSS MUTATED    41   1   1   0   2
  11P LOSS WILD-TYPE 135   1   1   2   1
D59V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  11P LOSS MUTATED   20  0   2   7  0   2   2   4  6  2
  11P LOSS WILD-TYPE 90  2   6  10  1   3  12   2 13  3
D59V7, multiclass
D59V8, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11P LOSS MUTATED             1       1        1        6        2         0
  11P LOSS WILD-TYPE           3      16        9        9       18         9
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11P LOSS MUTATED           3         4         1          2          9
  11P LOSS WILD-TYPE         7        19         8          5         12
                    vv
clus                 STAGE IIIC STAGE IV
  11P LOSS MUTATED           10        4
  11P LOSS WILD-TYPE         17        3
D59V9, multiclass

Clustering(60) Variable = 11q loss mutation analysis
D60V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   18 16
  11Q LOSS WILD-TYPE 41 39
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                34                 80 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                16                 39 
$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 
        2.86         3.88        48.79        35.80        39.19        44.52 
TCGA-DA-A1I8 TCGA-EB-A24D TCGA-EB-A3XB TCGA-EB-A3Y6 TCGA-EE-A182 TCGA-EE-A29C 
       25.15         1.35         1.18         0.53         1.35        37.97 
TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A2A2 
       11.15         1.08        27.12         8.12         8.84        23.90 
TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FW-A3I3 
        9.67         3.52        12.99         1.71         5.95         0.20 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        16.21        12.16        14.70 

$`11Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-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-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XC TCGA-EB-A3XF 
       14.83         0.53         0.43         1.28         0.30         0.13 
TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z 
        0.26         0.10         0.20         0.39        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
        1.12        12.20         4.27        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S 
        7.96        38.63         4.41         9.47        12.03         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 
        6.48         2.43         8.09        11.31        25.28         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       11.11         4.18        28.64        42.84        78.44         6.58 
TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 
       12.10        10.09        72.16        24.00         8.81        53.82 
TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 
        3.22        10.78         6.41         1.02         0.13        15.35 
TCGA-GN-A262 TCGA-GN-A263 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A269 
       24.85        15.35        84.72        10.09        15.39         5.59 
TCGA-GN-A26C TCGA-IH-A3EA 
       24.00        12.59 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               0.2                0.1 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             98.76              84.72 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            11.655             10.090 
[1] "0.2 - 98.8 (11.7)" "0.1 - 84.7 (10.1)"
        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-D9-A3Z4 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        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-D9-A3Z4 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        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-D9-A3Z4 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D60V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11Q LOSS MUTATED                    9             7
  11Q LOSS WILD-TYPE                 18            19
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11Q LOSS MUTATED                                                                                         10
  11Q LOSS WILD-TYPE                                                                                       27
                    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                                                                                           7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               10
  REGIONAL LYMPH NODE                                                                                    29
                                                                                          clus
vv                                                                                         11Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       18
  PRIMARY TUMOR                                                                                            19
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 27
  REGIONAL LYMPH NODE                                                                                      83
D60V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     26   29
  11Q LOSS WILD-TYPE   50   97
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               26                 50
  MALE                 29                 97
D60V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   55
  11Q LOSS WILD-TYPE    3  144
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 0                  3
  YES               55                144
                    vv
clus                  M0  M1 M1A M1B M1C
  11Q LOSS MUTATED    45   1   1   0   2
  11Q LOSS WILD-TYPE 131   1   1   2   1
D60V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  11Q LOSS MUTATED   26  0   2   7  0   2   2   4  5  2
  11Q LOSS WILD-TYPE 84  2   6  10  1   3  12   2 14  3
D60V7, multiclass
D60V8, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11Q LOSS MUTATED             1       2        1        7        2         0
  11Q LOSS WILD-TYPE           3      15        9        8       18         9
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11Q LOSS MUTATED           4         7         1          2          9
  11Q LOSS WILD-TYPE         6        16         8          5         12
                    vv
clus                 STAGE IIIC STAGE IV
  11Q LOSS MUTATED            9        4
  11Q LOSS WILD-TYPE         18        3
D60V9, multiclass

Clustering(61) Variable = 12p loss mutation analysis
D61V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    6  1
  12P LOSS WILD-TYPE 53 54
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 7                107 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 54 
$`12P LOSS MUTATED`
TCGA-D3-A2J6 TCGA-DA-A1I1 TCGA-EB-A24D TCGA-EB-A3Y6 TCGA-EE-A29Q TCGA-EE-A29S 
       10.26        39.19         1.35         0.53         8.12         9.99 
TCGA-EE-A2A2 
       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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2.86         3.88        48.79        35.80        51.12        10.03 
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-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF 
        0.53         0.43         1.28         1.18         0.30         0.13 
TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z 
        0.26         0.10         0.20         0.39        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-A29R TCGA-EE-A29T 
        1.08        27.12         9.47        12.03         8.84         6.48 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
        2.43         8.09        11.31        25.28         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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN 
       78.44         6.58         1.71        12.10        10.09         5.95 
TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
       72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       15.35        31.33        84.72        10.09        16.21        15.39 
TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
        5.59        12.16        24.00        14.70        12.59 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.53               0.10 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             39.19              98.76 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              9.99              11.11 
[1] "0.5 - 39.2 (10.0)" "0.1 - 98.8 (11.1)"
        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-D9-A3Z4 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr=" "2.9"
D61V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12P LOSS MUTATED                    2             2
  12P LOSS WILD-TYPE                 25            24
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12P LOSS MUTATED                                                                                          4
  12P LOSS WILD-TYPE                                                                                       33
                    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                                                                                           2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         12P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       25
  PRIMARY TUMOR                                                                                            24
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 33
  REGIONAL LYMPH NODE                                                                                     107
D61V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      6    7
  12P LOSS WILD-TYPE   70  119
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                6                 70
  MALE                  7                119
D61V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   12
  12P LOSS WILD-TYPE    2  187
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 1                  2
  YES               12                187
                    vv
clus                  M0  M1 M1A M1B M1C
  12P LOSS MUTATED    11   0   0   0   1
  12P LOSS WILD-TYPE 165   2   2   2   2
D61V6, multiclass
                    vv
clus                  N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  12P LOSS MUTATED     7   0   0   1   0   0   2   2   1   0
  12P LOSS WILD-TYPE 103   2   8  16   1   5  12   4  18   5
D61V7, multiclass
D61V8, 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       15       19         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12P LOSS MUTATED           2         1         0          0          3
  12P LOSS WILD-TYPE         8        22         9          7         18
                    vv
clus                 STAGE IIIC STAGE IV
  12P LOSS MUTATED            1        1
  12P LOSS WILD-TYPE         26        6
D61V9, multiclass

Clustering(62) Variable = 12q loss mutation analysis
D62V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    9  5
  12Q LOSS WILD-TYPE 50 50
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                14                100 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 5                 50 
$`12Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-DA-A1I1 TCGA-EB-A1NK TCGA-EB-A24D 
       16.47        10.26        45.70        39.19         0.53         1.35 
TCGA-EB-A3Y6 TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 
        0.53         8.12         9.99         8.09        23.90         9.67 
TCGA-ER-A3PL TCGA-FS-A4F2 
        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-D9-A3Z4 
       24.00         9.30         5.39         4.01         2.86         3.88 
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-EB-A24C TCGA-EB-A3HV 
       19.36         7.00        17.56        14.83         0.43         1.28 
TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y 
        1.18         0.30         0.13         0.26         0.10         0.20 
TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.39        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-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 
       12.03         8.84         6.48         2.43        11.31        25.28 
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-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN 
       42.84        78.44         6.58        12.10        10.09         5.95 
TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
       72.16        24.00         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-A263 
        0.20         1.02         0.13        15.35        24.85        15.35 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 
       31.33        84.72        10.09        16.21        15.39         5.59 
TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       12.16        24.00        14.70        12.59 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.53               0.10 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             45.70              98.76 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             8.895             11.230 
[1] "0.5 - 45.7 (8.9)"  "0.1 - 98.8 (11.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "12Q LOSS 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-D9-A3Z4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED"   "12Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "12Q LOSS 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-D9-A3Z4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED"   "12Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "12Q LOSS 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-D9-A3Z4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED"   "12Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D62V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12Q LOSS MUTATED                    3             4
  12Q LOSS WILD-TYPE                 24            22
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12Q LOSS MUTATED                                                                                          8
  12Q LOSS WILD-TYPE                                                                                       29
                    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                                                                                           4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                     9
                                                                                          clus
vv                                                                                         12Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       24
  PRIMARY TUMOR                                                                                            22
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 29
  REGIONAL LYMPH NODE                                                                                     103
D62V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     12   12
  12Q LOSS WILD-TYPE   64  114
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               12                 64
  MALE                 12                114
D62V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   23
  12Q LOSS WILD-TYPE    2  176
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 1                  2
  YES               23                176
                    vv
clus                  M0  M1 M1A M1B M1C
  12Q LOSS MUTATED    20   0   1   0   1
  12Q LOSS WILD-TYPE 156   2   1   2   2
D62V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  12Q LOSS MUTATED   16  0   0   1  0   0   2   2  2  0
  12Q LOSS WILD-TYPE 94  2   8  16  1   5  12   4 17  5
D62V7, multiclass
D62V8, 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         2
  12Q LOSS WILD-TYPE           3      16        9       13       18         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12Q LOSS MUTATED           2         4         0          0          3
  12Q LOSS WILD-TYPE         8        19         9          7         18
                    vv
clus                 STAGE IIIC STAGE IV
  12Q LOSS MUTATED            2        2
  12Q LOSS WILD-TYPE         25        5
D62V9, multiclass

Clustering(63) Variable = 13q loss mutation analysis
D63V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   11 10
  13Q LOSS WILD-TYPE 48 45
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                21                 93 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                10                 45 
$`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-EB-A3XB TCGA-EB-A3XC TCGA-EB-A41B TCGA-EE-A181 TCGA-EE-A29C 
        6.64         1.18         0.30         0.10         1.12        37.97 
TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T TCGA-FR-A3YN 
       11.15        27.12         9.47         8.12         6.48         5.95 
TCGA-GN-A266 TCGA-GN-A26C TCGA-GN-A26D 
       10.09        24.00        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-D9-A3Z4 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I5 
        3.88        35.80        51.12        10.03        39.19        44.52 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       36.69         4.93        22.36        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XF 
       14.83         0.53         0.43         1.35         1.28         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z 
        0.53         0.26         0.20         0.39        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-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R 
        7.96        38.63         4.41         1.08        12.03         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-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A2OS 
       28.64        42.84        78.44         6.58         1.71        12.10 
TCGA-FR-A3R1 TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 
       10.09        72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       24.85        15.35        31.33        84.72        16.21        15.39 
TCGA-GN-A269 TCGA-GN-A26A TCGA-IH-A3EA 
        5.59        12.16        12.59 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.10               0.13 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             48.79              98.76 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              9.99              11.11 
[1] "0.1 - 48.8 (10.0)" "0.1 - 98.8 (11.1)"
        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-D9-A3Z4 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        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-D9-A3Z4 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        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-D9-A3Z4 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D63V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  13Q LOSS MUTATED                    1             6
  13Q LOSS WILD-TYPE                 26            20
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  13Q LOSS MUTATED                                                                                          5
  13Q LOSS WILD-TYPE                                                                                       32
                    vv
clus                 REGIONAL LYMPH NODE
  13Q LOSS MUTATED                    17
  13Q LOSS WILD-TYPE                  95
D63V3, multiclass
                                                                                          clus
vv                                                                                         13Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    17
                                                                                          clus
vv                                                                                         13Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       26
  PRIMARY TUMOR                                                                                            20
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                      95
D63V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11   18
  13Q LOSS WILD-TYPE   65  108
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               11                 65
  MALE                 18                108
D63V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   28
  13Q LOSS WILD-TYPE    2  171
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 1                  2
  YES               28                171
                    vv
clus                  M0  M1 M1A M1B M1C
  13Q LOSS MUTATED    23   0   0   2   1
  13Q LOSS WILD-TYPE 153   2   2   0   2
D63V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  13Q LOSS MUTATED   12  0   0   2  0   0   4   4  3  2
  13Q LOSS WILD-TYPE 98  2   8  15  1   5  10   2 16  3
D63V7, multiclass
D63V8, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  13Q LOSS MUTATED             0       0        1        3        4         0
  13Q LOSS WILD-TYPE           4      17        9       12       16         9
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  13Q LOSS MUTATED           1         3         0          0          6
  13Q LOSS WILD-TYPE         9        20         9          7         15
                    vv
clus                 STAGE IIIC STAGE IV
  13Q LOSS MUTATED            4        2
  13Q LOSS WILD-TYPE         23        5
D63V9, multiclass

Clustering(64) Variable = 14q loss mutation analysis
D64V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   15 13
  14Q LOSS WILD-TYPE 44 42
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                28                 86 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                13                 42 
$`14Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D9-A3Z4 TCGA-DA-A1HV 
       16.47        10.26        45.70        13.32         3.88        48.79 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-EB-A24D TCGA-EB-A3Y6 
       51.12        39.19        44.52        17.56         1.35         0.53 
TCGA-EB-A41A TCGA-EB-A41B TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29V TCGA-EE-A29X 
        0.26         0.10         1.12        37.97         2.43         8.09 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A3PL TCGA-FS-A1ZR TCGA-FS-A4F2 TCGA-FS-A4F9 
        9.67         8.94         1.71         8.81         3.22        10.78 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       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-EB-A1NK TCGA-EB-A24C 
        6.64        19.36         7.00        14.83         0.53         0.43 
TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A42Y TCGA-EB-A42Z 
        1.28         1.18         0.30         0.13         0.20         0.39 
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-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-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19D 
        9.99         6.48        11.31        25.28        23.90         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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN 
        6.58        12.10        10.09         5.95        72.16        24.00 
TCGA-FS-A4F0 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 
       53.82         6.41         0.20         1.02         0.13        15.35 
TCGA-GN-A262 TCGA-GN-A263 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A269 TCGA-GN-A26C 
       24.85        15.35        84.72        10.09         5.59        24.00 
TCGA-GN-A26D TCGA-IH-A3EA 
       14.70        12.59 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.10               0.13 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             51.12              98.76 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             10.52              10.60 
[1] "0.1 - 51.1 (10.5)" "0.1 - 98.8 (10.6)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "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-D9-A3Z4 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "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-D9-A3Z4 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  14Q LOSS MUTATED                    7             5
  14Q LOSS WILD-TYPE                 20            21
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  14Q LOSS MUTATED                                                                                         10
  14Q LOSS WILD-TYPE                                                                                       27
                    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                                                                                           5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               10
  REGIONAL LYMPH NODE                                                                                    25
                                                                                          clus
vv                                                                                         14Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       20
  PRIMARY TUMOR                                                                                            21
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 27
  REGIONAL LYMPH NODE                                                                                      87
D64V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     17   30
  14Q LOSS WILD-TYPE   59   96
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               17                 59
  MALE                 30                 96
D64V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      0   47
  14Q LOSS WILD-TYPE    3  152
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 0                  3
  YES               47                152
                    vv
clus                  M0  M1 M1A M1B M1C
  14Q LOSS MUTATED    43   0   1   0   2
  14Q LOSS WILD-TYPE 133   2   1   2   1
D64V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  14Q LOSS MUTATED   28  0   3   4  0   0   2   3  6  0
  14Q LOSS WILD-TYPE 82  2   5  13  1   5  12   3 13  5
D64V7, multiclass
D64V8, 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       12       12         9
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  14Q LOSS MUTATED           2         6         2          2          4
  14Q LOSS WILD-TYPE         8        17         7          5         17
                    vv
clus                 STAGE IIIC STAGE IV
  14Q LOSS MUTATED            8        3
  14Q LOSS WILD-TYPE         19        4
D64V9, multiclass

Clustering(65) Variable = 15q loss mutation analysis
D65V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    2  4
  15Q LOSS WILD-TYPE 57 51
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                108 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                 51 
$`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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2.86         3.88        48.79        35.80        51.12        10.03 
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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC 
        0.53         0.43         1.35         1.28         1.18         0.30 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z 
        0.13         0.53         0.26         0.10         0.20         0.39 
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-A29Q TCGA-EE-A29R 
       38.63         4.41        27.12         9.47         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-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       23.90         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-A2OS 
       28.64        42.84        78.44         6.58         1.71        12.10 
TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 
       10.09         5.95        72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       15.35        24.85        15.35        31.33        84.72        16.21 
TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       15.39         5.59        12.16        24.00        14.70        12.59 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              1.08               0.10 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             39.19              98.76 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             11.06              10.52 
[1] "1.1 - 39.2 (11.1)" "0.1 - 98.8 (10.5)"
        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-D9-A3Z4 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D65V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  15Q LOSS MUTATED                    1             0
  15Q LOSS WILD-TYPE                 26            26
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  15Q LOSS MUTATED                                                                                          5
  15Q LOSS WILD-TYPE                                                                                       32
                    vv
clus                 REGIONAL LYMPH NODE
  15Q LOSS MUTATED                     6
  15Q LOSS WILD-TYPE                 106
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                                                                                     6
                                                                                          clus
vv                                                                                         15Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       26
  PRIMARY TUMOR                                                                                            26
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                     106
D65V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5    7
  15Q LOSS WILD-TYPE   71  119
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                5                 71
  MALE                  7                119
D65V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0   12
  15Q LOSS WILD-TYPE    3  187
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 0                  3
  YES               12                187
                    vv
clus                  M0  M1 M1A M1B M1C
  15Q LOSS MUTATED     9   0   0   1   0
  15Q LOSS WILD-TYPE 167   2   2   1   3
D65V6, 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 104   2   8  17   1   5  14   5  16   5
D65V7, multiclass
D65V8, 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       13       19         9
                    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        22         8          7         21
                    vv
clus                 STAGE IIIC STAGE IV
  15Q LOSS MUTATED            2        0
  15Q LOSS WILD-TYPE         25        7
D65V9, multiclass

Clustering(66) Variable = 16p loss mutation analysis
D66V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    4  8
  16P LOSS WILD-TYPE 55 47
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                12                102 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 8                 47 
$`16P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EB-A24D TCGA-EB-A3XC TCGA-EE-A17Z 
       32.55        35.80        13.68         1.35         0.30         6.31 
TCGA-EE-A29D TCGA-EE-A29X TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 
       11.15         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-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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        2.86         3.88        48.79        51.12        10.03        39.19 
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-EB-A1NK 
        6.64        19.36         7.00        17.56        14.83         0.53 
TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A 
        0.43         1.28         1.18         0.13         0.53         0.26 
TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
        0.10         0.20         0.39        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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A 
        6.58         1.71        12.10        10.09         5.95        72.16 
TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC 
       24.00         8.81        53.82         3.22        10.78         6.41 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A263 TCGA-GN-A265 TCGA-GN-A266 
        0.20         1.02        15.35        15.35        84.72        10.09 
TCGA-GN-A267 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       16.21         5.59        12.16        24.00        14.70        12.59 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.13               0.10 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             35.80              98.76 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            12.415             10.175 
[1] "0.1 - 35.8 (12.4)" "0.1 - 98.8 (10.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D66V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16P LOSS MUTATED                    2             2
  16P LOSS WILD-TYPE                 25            24
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16P LOSS MUTATED                                                                                          1
  16P LOSS WILD-TYPE                                                                                       36
                    vv
clus                 REGIONAL LYMPH NODE
  16P LOSS MUTATED                    10
  16P LOSS WILD-TYPE                 102
D66V3, multiclass
                                                                                          clus
vv                                                                                         16P LOSS MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                    10
                                                                                          clus
vv                                                                                         16P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       25
  PRIMARY TUMOR                                                                                            24
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 36
  REGIONAL LYMPH NODE                                                                                     102
D66V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7    8
  16P LOSS WILD-TYPE   69  118
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                7                 69
  MALE                  8                118
D66V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0   15
  16P LOSS WILD-TYPE    3  184
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 0                  3
  YES               15                184
                    vv
clus                  M0  M1 M1A M1B M1C
  16P LOSS MUTATED    12   0   0   0   0
  16P LOSS WILD-TYPE 164   2   2   2   3
D66V6, multiclass
                    vv
clus                  N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  16P LOSS MUTATED     8   0   0   2   0   0   2   0   0   0
  16P LOSS WILD-TYPE 102   2   8  15   1   5  12   6  19   5
D66V7, multiclass
D66V8, 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       14       19         9
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16P LOSS MUTATED           3         2         0          0          2
  16P LOSS WILD-TYPE         7        21         9          7         19
                    vv
clus                 STAGE IIIC STAGE IV
  16P LOSS MUTATED            2        0
  16P LOSS WILD-TYPE         25        7
D66V9, multiclass

Clustering(67) Variable = 16q loss mutation analysis
D67V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   11 14
  16Q LOSS WILD-TYPE 48 41
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                25                 89 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                 41 
$`16Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A2JF TCGA-D9-A3Z3 TCGA-D9-A3Z4 TCGA-DA-A1HW TCGA-DA-A1I2 
       32.55        30.87         2.86         3.88        35.80        13.68 
TCGA-DA-A1I4 TCGA-DA-A3F8 TCGA-EB-A24D TCGA-EB-A3XC TCGA-EB-A3Y6 TCGA-EB-A41B 
        9.99        14.83         1.35         0.30         0.53         0.10 
TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A29D TCGA-EE-A29X TCGA-EE-A2A5 TCGA-FS-A4F2 
        6.31         4.27        11.15         8.09         9.67         3.22 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
        0.20         0.13        24.85        31.33        16.21        15.39 
TCGA-GN-A269 
        5.59 

$`16Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HV 
       13.32        24.00         9.30         5.39         4.01        48.79 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       51.12        10.03        39.19        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XF TCGA-EB-A41A 
        0.53         0.43         1.28         1.18         0.13         0.26 
TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.20         0.39        11.57         1.12         1.35        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       36.07         5.13         8.81         7.96        37.97        38.63 
TCGA-EE-A29H TCGA-EE-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-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         9.99         6.48         2.43        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       23.90         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-A2OS 
       28.64        42.84        78.44         6.58         1.71        12.10 
TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 
       10.09         5.95        72.16        24.00         8.81        53.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A263 TCGA-GN-A265 
       10.78         6.41         1.02        15.35        15.35        84.72 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       10.09        12.16        24.00        14.70        12.59 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.10               0.13 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             35.80              98.76 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              8.09              11.31 
[1] "0.1 - 35.8 (8.1)"  "0.1 - 98.8 (11.3)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D67V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16Q LOSS MUTATED                    7             7
  16Q LOSS WILD-TYPE                 20            19
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16Q LOSS MUTATED                                                                                          6
  16Q LOSS WILD-TYPE                                                                                       31
                    vv
clus                 REGIONAL LYMPH NODE
  16Q LOSS MUTATED                    18
  16Q LOSS WILD-TYPE                  94
D67V3, multiclass
                                                                                          clus
vv                                                                                         16Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      7
  PRIMARY TUMOR                                                                                           7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                    18
                                                                                          clus
vv                                                                                         16Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       20
  PRIMARY TUMOR                                                                                            19
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 31
  REGIONAL LYMPH NODE                                                                                      94
D67V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     15   23
  16Q LOSS WILD-TYPE   61  103
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               15                 61
  MALE                 23                103
D67V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0   38
  16Q LOSS WILD-TYPE    3  161
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 0                  3
  YES               38                161
                    vv
clus                  M0  M1 M1A M1B M1C
  16Q LOSS MUTATED    32   1   0   1   0
  16Q LOSS WILD-TYPE 144   1   2   1   3
D67V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  16Q LOSS MUTATED   20  0   2   4  0   0   4   0  4  0
  16Q LOSS WILD-TYPE 90  2   6  13  1   5  10   6 15  5
D67V7, multiclass
D67V8, 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       13       16         9
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16Q LOSS MUTATED           3         8         0          1          6
  16Q LOSS WILD-TYPE         7        15         9          6         15
                    vv
clus                 STAGE IIIC STAGE IV
  16Q LOSS MUTATED            5        1
  16Q LOSS WILD-TYPE         22        6
D67V9, multiclass

Clustering(68) Variable = 17p loss mutation analysis
D68V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   16 10
  17P LOSS WILD-TYPE 43 45
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                26                 88 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                10                 45 
$`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-EB-A1NK TCGA-EB-A3XC TCGA-EB-A41B TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29H 
        0.53         0.30         0.10         4.27        37.97         4.41 
TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
       27.12         9.99         6.48         2.43         8.09        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-FR-A3YN TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FW-A3I3 
       23.90         9.67         5.95         3.22        10.78         0.20 
TCGA-FW-A3R5 TCGA-GN-A266 
        1.02        10.09 

$`17P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-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-D9-A3Z4 TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
        3.88        10.03        39.19        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-A3F5 TCGA-DA-A3F8 TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
       17.56        14.83         0.43         1.35         1.28         1.18 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X 
        0.13         0.53         0.26         0.20         0.39        11.57 
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-A29E TCGA-EE-A29L TCGA-EE-A29N 
        8.81         7.96        11.15        38.63         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-ER-A19D 
       12.03         8.12         8.84        11.31         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-A2OS TCGA-FR-A3R1 TCGA-FR-A44A TCGA-FS-A1ZN 
        6.58         1.71        12.10        10.09        72.16        24.00 
TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4FC TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 
        8.81        53.82         6.41         0.13        15.35        24.85 
TCGA-GN-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 
       15.35        31.33        84.72        16.21        15.39         5.59 
TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       12.16        24.00        14.70        12.59 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.10               0.13 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             51.12              98.76 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             8.695             11.800 
[1] "0.1 - 51.1 (8.7)"  "0.1 - 98.8 (11.8)"
        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-D9-A3Z4 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D68V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17P LOSS MUTATED                    5             5
  17P LOSS WILD-TYPE                 22            21
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17P LOSS MUTATED                                                                                          5
  17P LOSS WILD-TYPE                                                                                       32
                    vv
clus                 REGIONAL LYMPH NODE
  17P LOSS MUTATED                    26
  17P LOSS WILD-TYPE                  86
D68V3, multiclass
                                                                                          clus
vv                                                                                         17P LOSS MUTATED
  DISTANT METASTASIS                                                                                      5
  PRIMARY TUMOR                                                                                           5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    26
                                                                                          clus
vv                                                                                         17P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       22
  PRIMARY TUMOR                                                                                            21
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                      86
D68V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     14   27
  17P LOSS WILD-TYPE   62   99
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               14                 62
  MALE                 27                 99
D68V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      0   41
  17P LOSS WILD-TYPE    3  158
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 0                  3
  YES               41                158
                    vv
clus                  M0  M1 M1A M1B M1C
  17P LOSS MUTATED    37   1   0   1   1
  17P LOSS WILD-TYPE 139   1   2   1   2
D68V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  17P LOSS MUTATED   25  0   1   3  1   1   2   2  4  1
  17P LOSS WILD-TYPE 85  2   7  14  0   4  12   4 15  4
D68V7, multiclass
D68V8, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17P LOSS MUTATED             1       4        3        6        0         2
  17P LOSS WILD-TYPE           3      13        7        9       20         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17P LOSS MUTATED           3         5         2          1          5
  17P LOSS WILD-TYPE         7        18         7          6         16
                    vv
clus                 STAGE IIIC STAGE IV
  17P LOSS MUTATED            4        2
  17P LOSS WILD-TYPE         23        5
D68V9, multiclass

Clustering(69) Variable = 17q loss mutation analysis
D69V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    6  6
  17Q LOSS WILD-TYPE 53 49
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                102 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                 49 
$`17Q LOSS MUTATED`
TCGA-D3-A2J6 TCGA-DA-A1HW TCGA-EB-A3XC TCGA-EB-A41B TCGA-EE-A29C TCGA-EE-A29X 
       10.26        35.80         0.30         0.10        37.97         8.09 
TCGA-EE-A2A5 TCGA-ER-A19L TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FW-A3I3 TCGA-FW-A3R5 
        9.67        12.99         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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        2.86         3.88        48.79        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XF 
        0.53         0.43         1.35         1.28         1.18         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z 
        0.53         0.26         0.20         0.39        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-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        6.48         2.43        11.31        25.28        23.90         8.94 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
        3.52        11.11         4.18        28.64        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A 
        6.58         1.71        12.10        10.09         5.95        72.16 
TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4FC TCGA-FW-A3TU TCGA-GN-A261 
       24.00         8.81        53.82         6.41         0.13        15.35 
TCGA-GN-A262 TCGA-GN-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       24.85        15.35        31.33        84.72        10.09        16.21 
TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       15.39         5.59        12.16        24.00        14.70        12.59 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.10               0.13 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             37.97              98.76 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              8.88              11.23 
[1] "0.1 - 38.0 (8.9)"  "0.1 - 98.8 (11.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D69V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17Q LOSS MUTATED                    3             2
  17Q LOSS WILD-TYPE                 24            24
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17Q LOSS MUTATED                                                                                          2
  17Q LOSS WILD-TYPE                                                                                       35
                    vv
clus                 REGIONAL LYMPH NODE
  17Q LOSS MUTATED                    13
  17Q LOSS WILD-TYPE                  99
D69V3, multiclass
                                                                                          clus
vv                                                                                         17Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      3
  PRIMARY TUMOR                                                                                           2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                    13
                                                                                          clus
vv                                                                                         17Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       24
  PRIMARY TUMOR                                                                                            24
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 35
  REGIONAL LYMPH NODE                                                                                      99
D69V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      7   13
  17Q LOSS WILD-TYPE   69  113
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                7                 69
  MALE                 13                113
D69V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0   20
  17Q LOSS WILD-TYPE    3  179
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 0                  3
  YES               20                179
                    vv
clus                  M0  M1 M1A M1B M1C
  17Q LOSS MUTATED    17   1   0   0   1
  17Q LOSS WILD-TYPE 159   1   2   2   2
D69V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  17Q LOSS MUTATED   13  0   1   1  1   1   0   1  1  0
  17Q LOSS WILD-TYPE 97  2   7  16  0   4  14   5 18  5
D69V7, multiclass
D69V8, 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       12       20         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17Q LOSS MUTATED           2         3         1          1          2
  17Q LOSS WILD-TYPE         8        20         8          6         19
                    vv
clus                 STAGE IIIC STAGE IV
  17Q LOSS MUTATED            1        2
  17Q LOSS WILD-TYPE         26        5
D69V9, multiclass

Clustering(70) Variable = 18p loss mutation analysis
D70V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    9  9
  18P LOSS WILD-TYPE 50 46
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                18                 96 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 9                 46 
$`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-EB-A3Y6 TCGA-EB-A42Z TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29D 
       17.56         0.53         0.39        36.07         7.96        11.15 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-FS-A1ZR TCGA-FW-A3TU 
       27.12         6.48         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-D9-A3Z4 
       24.00         9.30         5.39         4.01         2.86         3.88 
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-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-A3F8 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
       14.83         0.53         0.43         1.35         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EE-A17X 
        0.30         0.13         0.26         0.10         0.20        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
        6.31         1.12         1.35        12.20         4.27         5.13 
TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
        8.81        37.97        38.63         4.41         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 
       12.03         8.12         8.84         9.99        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J 
       23.90         9.67         8.94         3.52        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL 
       12.99        28.64        42.84        78.44         6.58         1.71 
TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A4F0 
       12.10        10.09         5.95        72.16        24.00        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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       24.85        15.35        31.33        84.72        10.09        16.21 
TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       15.39         5.59        12.16        24.00        14.70        12.59 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.13               0.10 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             70.16              98.76 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            12.415             10.175 
[1] "0.1 - 70.2 (12.4)" "0.1 - 98.8 (10.2)"
        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-D9-A3Z4 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D70V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18P LOSS MUTATED                    7             4
  18P LOSS WILD-TYPE                 20            22
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18P LOSS MUTATED                                                                                          9
  18P LOSS WILD-TYPE                                                                                       28
                    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                                                                                           4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                9
  REGIONAL LYMPH NODE                                                                                    19
                                                                                          clus
vv                                                                                         18P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       20
  PRIMARY TUMOR                                                                                            22
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 28
  REGIONAL LYMPH NODE                                                                                      93
D70V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     16   23
  18P LOSS WILD-TYPE   60  103
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               16                 60
  MALE                 23                103
D70V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1   38
  18P LOSS WILD-TYPE    2  161
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 1                  2
  YES               38                161
                    vv
clus                  M0  M1 M1A M1B M1C
  18P LOSS MUTATED    35   0   0   0   0
  18P LOSS WILD-TYPE 141   2   2   2   3
D70V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  18P LOSS MUTATED   18  0   3   4  0   1   4   2  2  2
  18P LOSS WILD-TYPE 92  2   5  13  1   4  10   4 17  3
D70V7, multiclass
D70V8, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18P LOSS MUTATED             2       1        2        4        7         0
  18P LOSS WILD-TYPE           2      16        8       11       13         9
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18P LOSS MUTATED           1         1         2          2          5
  18P LOSS WILD-TYPE         9        22         7          5         16
                    vv
clus                 STAGE IIIC STAGE IV
  18P LOSS MUTATED            6        0
  18P LOSS WILD-TYPE         21        7
D70V9, multiclass

Clustering(71) Variable = 18q loss mutation analysis
D71V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    8 11
  18Q LOSS WILD-TYPE 51 44
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                19                 95 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                11                 44 
$`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-EB-A42Z TCGA-EE-A20B 
       13.68        36.69         4.93        17.56         0.39        36.07 
TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X 
        7.96        11.15        27.12         6.48         2.43         8.09 
TCGA-FW-A3TU 
        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-D9-A3Z4 TCGA-DA-A1HW TCGA-DA-A1HY 
        5.39         4.01         2.86         3.88        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB 
       10.03        39.19         9.99        44.52        25.15        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A1NK TCGA-EB-A24C 
        6.64        19.36         7.00        14.83         0.53         0.43 
TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 
        1.35         1.28         1.18         0.30         0.13         0.53 
TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        0.26         0.10         0.20        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-A2OS TCGA-FR-A3R1 
       42.84        78.44         6.58         1.71        12.10        10.09 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 
        5.95        72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       15.35        31.33        84.72        10.09        16.21        15.39 
TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
        5.59        12.16        24.00        14.70        12.59 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.13               0.10 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             70.16              98.76 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             13.68              10.09 
[1] "0.1 - 70.2 (13.7)" "0.1 - 98.8 (10.1)"
        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-D9-A3Z4 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D71V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18Q LOSS MUTATED                    7             3
  18Q LOSS WILD-TYPE                 20            23
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18Q LOSS MUTATED                                                                                          7
  18Q LOSS WILD-TYPE                                                                                       30
                    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                                                                                           3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                7
  REGIONAL LYMPH NODE                                                                                    19
                                                                                          clus
vv                                                                                         18Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       20
  PRIMARY TUMOR                                                                                            23
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                      93
D71V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     14   22
  18Q LOSS WILD-TYPE   62  104
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               14                 62
  MALE                 22                104
D71V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1   35
  18Q LOSS WILD-TYPE    2  164
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 1                  2
  YES               35                164
                    vv
clus                  M0  M1 M1A M1B M1C
  18Q LOSS MUTATED    32   0   0   1   0
  18Q LOSS WILD-TYPE 144   2   2   1   3
D71V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  18Q LOSS MUTATED   14  0   3   6  0   2   4   1  3  1
  18Q LOSS WILD-TYPE 96  2   5  11  1   3  10   5 16  4
D71V7, multiclass
D71V8, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18Q LOSS MUTATED             2       0        2        4        5         0
  18Q LOSS WILD-TYPE           2      17        8       11       15         9
                    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        23         6          5         15
                    vv
clus                 STAGE IIIC STAGE IV
  18Q LOSS MUTATED            6        0
  18Q LOSS WILD-TYPE         21        7
D71V9, multiclass

Clustering(72) Variable = 19p loss mutation analysis
D72V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    4  6
  19P LOSS WILD-TYPE 55 49
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                10                104 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 6                 49 
$`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-EB-A3XC TCGA-EE-A29H TCGA-EE-A29X TCGA-EE-A2A0 
        0.30         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-D9-A3Z4 
       13.32        24.00         9.30         5.39         4.01         3.88 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       51.12        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV 
       17.56        14.83         0.53         0.43         1.35         1.28 
TCGA-EB-A3XB TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y 
        1.18         0.13         0.53         0.26         0.10         0.20 
TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.39        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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR 
       12.10        10.09         5.95        72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 
        0.13        15.35        24.85        15.35        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C 
       10.09        16.21        15.39         5.59        12.16        24.00 
TCGA-GN-A26D TCGA-IH-A3EA 
       14.70        12.59 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               0.3                0.1 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             48.79              98.76 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            13.890             10.175 
[1] "0.3 - 48.8 (13.9)" "0.1 - 98.8 (10.2)"
        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-D9-A3Z4 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D72V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19P LOSS MUTATED                    1             2
  19P LOSS WILD-TYPE                 26            24
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19P LOSS MUTATED                                                                                          3
  19P LOSS WILD-TYPE                                                                                       34
                    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                                                                                           2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                    12
                                                                                          clus
vv                                                                                         19P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       26
  PRIMARY TUMOR                                                                                            24
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 34
  REGIONAL LYMPH NODE                                                                                     100
D72V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     10    8
  19P LOSS WILD-TYPE   66  118
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               10                 66
  MALE                  8                118
D72V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   18
  19P LOSS WILD-TYPE    3  181
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 0                  3
  YES               18                181
                    vv
clus                  M0  M1 M1A M1B M1C
  19P LOSS MUTATED    15   0   0   1   1
  19P LOSS WILD-TYPE 161   2   2   1   2
D72V6, multiclass
                    vv
clus                  N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  19P LOSS MUTATED     7   0   1   2   0   1   2   1   3   0
  19P LOSS WILD-TYPE 103   2   7  15   1   4  12   5  16   5
D72V7, multiclass
D72V8, 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       14       20         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19P LOSS MUTATED           0         3         1          0          5
  19P LOSS WILD-TYPE        10        20         8          7         16
                    vv
clus                 STAGE IIIC STAGE IV
  19P LOSS MUTATED            2        1
  19P LOSS WILD-TYPE         25        6
D72V9, multiclass

Clustering(73) Variable = 19q loss mutation analysis
D73V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    8  4
  19Q LOSS WILD-TYPE 51 51
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                102 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                 51 
$`19Q LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1I8 TCGA-EB-A1NK TCGA-EB-A3XC 
       22.55         2.86        48.79        25.15         0.53         0.30 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29S TCGA-EE-A29X TCGA-GN-A26A TCGA-GN-A26D 
        4.41        27.12         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-D9-A3Z4 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
        3.88        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
        9.99        44.52        36.69         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A24C TCGA-EB-A24D 
       19.36         7.00        17.56        14.83         0.43         1.35 
TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B 
        1.28         1.18         0.13         0.53         0.26         0.10 
TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
        0.20         0.39        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-A29N TCGA-EE-A29P 
       37.97        11.15        38.63         1.08         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.12         8.84         6.48         2.43        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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A1ZR 
       12.10        10.09         5.95        72.16        24.00         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-A263 TCGA-GN-A264 TCGA-GN-A265 
        0.13        15.35        24.85        15.35        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26C TCGA-IH-A3EA 
       10.09        16.21        15.39         5.59        24.00        12.59 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               0.3                0.1 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             48.79              98.76 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            11.075             10.520 
[1] "0.3 - 48.8 (11.1)" "0.1 - 98.8 (10.5)"
        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-D9-A3Z4 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        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-D9-A3Z4 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        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-D9-A3Z4 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D73V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19Q LOSS MUTATED                    0             4
  19Q LOSS WILD-TYPE                 27            22
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19Q LOSS MUTATED                                                                                          3
  19Q LOSS WILD-TYPE                                                                                       34
                    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                                                                                           4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                    12
                                                                                          clus
vv                                                                                         19Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       27
  PRIMARY TUMOR                                                                                            22
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 34
  REGIONAL LYMPH NODE                                                                                     100
D73V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      9   10
  19Q LOSS WILD-TYPE   67  116
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                9                 67
  MALE                 10                116
D73V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   19
  19Q LOSS WILD-TYPE    3  180
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 0                  3
  YES               19                180
                    vv
clus                  M0  M1 M1A M1B M1C
  19Q LOSS MUTATED    14   0   0   1   1
  19Q LOSS WILD-TYPE 162   2   2   1   2
D73V6, multiclass
                    vv
clus                  N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  19Q LOSS MUTATED     8   0   2   1   0   1   2   1   2   0
  19Q LOSS WILD-TYPE 102   2   6  16   1   4  12   5  17   5
D73V7, multiclass
D73V8, 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       13       20         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19Q LOSS MUTATED           0         4         1          1          4
  19Q LOSS WILD-TYPE        10        19         8          6         17
                    vv
clus                 STAGE IIIC STAGE IV
  19Q LOSS MUTATED            1        1
  19Q LOSS WILD-TYPE         26        6
D73V9, multiclass

Clustering(74) Variable = 20p loss mutation analysis
D74V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    4  2
  20P LOSS WILD-TYPE 55 53
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 6                108 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 53 
$`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-D9-A3Z4 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        2.86         3.88        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-EB-A1NK 
        6.64        19.36         7.00        17.56        14.83         0.53 
TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF 
        0.43         1.35         1.28         1.18         0.30         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X 
        0.53         0.26         0.10         0.20         0.39        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-A29H 
        5.13         8.81         7.96        37.97        11.15         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-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A2OS 
       12.99        28.64        42.84        78.44         6.58        12.10 
TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZN TCGA-FS-A4F0 TCGA-FS-A4F2 
       10.09         5.95        72.16        24.00        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-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       24.85        15.35        31.33        84.72        10.09        16.21 
TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       15.39         5.59        12.16        24.00        14.70        12.59 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              1.71               0.10 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             48.79              98.76 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            31.315             10.175 
[1] "1.7 - 48.8 (31.3)" "0.1 - 98.8 (10.2)"
        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-D9-A3Z4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
[1] "hr=" "2.5"
D74V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20P LOSS MUTATED                    1             0
  20P LOSS WILD-TYPE                 26            26
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20P LOSS MUTATED                                                                                          4
  20P LOSS WILD-TYPE                                                                                       33
                    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)                4
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         20P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       26
  PRIMARY TUMOR                                                                                            26
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 33
  REGIONAL LYMPH NODE                                                                                     109
D74V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2    6
  20P LOSS WILD-TYPE   74  120
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                2                 74
  MALE                  6                120
D74V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0    8
  20P LOSS WILD-TYPE    3  191
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 0                  3
  YES                8                191
                    vv
clus                  M0  M1 M1A M1B M1C
  20P LOSS MUTATED     7   0   1   0   0
  20P LOSS WILD-TYPE 169   2   1   2   3
D74V6, multiclass
                    vv
clus                  N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  20P LOSS MUTATED     4   0   0   1   0   0   1   0   2   0
  20P LOSS WILD-TYPE 106   2   8  16   1   5  13   6  17   5
D74V7, multiclass
D74V8, 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       15       19         9
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  20P LOSS MUTATED           0         2         0          0          2
  20P LOSS WILD-TYPE        10        21         9          7         19
                    vv
clus                 STAGE IIIC STAGE IV
  20P LOSS MUTATED            2        1
  20P LOSS WILD-TYPE         25        6
D74V9, multiclass

Clustering(75) Variable = 21q loss mutation analysis
D75V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    6  5
  21Q LOSS WILD-TYPE 53 50
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                11                103 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 5                 50 
$`21Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-EB-A24D TCGA-EB-A3XC TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29H 
       32.55         1.35         0.30         1.12        36.07         4.41 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-FS-A1ZN TCGA-GN-A266 TCGA-GN-A268 
       23.90         8.94        24.00        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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2.86         3.88        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XF 
       14.83         0.53         0.43         1.28         1.18         0.13 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X 
        0.53         0.26         0.10         0.20         0.39        11.57 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H 
        6.31         1.35        12.20         4.27         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M 
        7.96        37.97        11.15        38.63         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-A2A5 TCGA-ER-A19D 
        2.43         8.09        11.31        25.28         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-ER-A3PL TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A 
        6.58         1.71        12.10        10.09         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-A263 TCGA-GN-A264 
        1.02         0.13        15.35        24.85        15.35        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D 
       84.72        16.21         5.59        12.16        24.00        14.70 
TCGA-IH-A3EA 
       12.59 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               0.3                0.1 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             36.07              98.76 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             10.09              10.78 
[1] "0.3 - 36.1 (10.1)" "0.1 - 98.8 (10.8)"
        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-D9-A3Z4 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D75V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  21Q LOSS MUTATED                    3             3
  21Q LOSS WILD-TYPE                 24            23
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  21Q LOSS MUTATED                                                                                          3
  21Q LOSS WILD-TYPE                                                                                       34
                    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                                                                                           3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                    15
                                                                                          clus
vv                                                                                         21Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       24
  PRIMARY TUMOR                                                                                            23
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 34
  REGIONAL LYMPH NODE                                                                                      97
D75V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      9   15
  21Q LOSS WILD-TYPE   67  111
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                9                 67
  MALE                 15                111
D75V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      0   24
  21Q LOSS WILD-TYPE    3  175
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 0                  3
  YES               24                175
                    vv
clus                  M0  M1 M1A M1B M1C
  21Q LOSS MUTATED    23   0   0   0   0
  21Q LOSS WILD-TYPE 153   2   2   2   3
D75V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  21Q LOSS MUTATED   17  0   2   1  0   0   2   1  0  0
  21Q LOSS WILD-TYPE 93  2   6  16  1   5  12   5 19  5
D75V7, multiclass
D75V8, 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       15       14         9
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  21Q LOSS MUTATED           2         3         0          2          3
  21Q LOSS WILD-TYPE         8        20         9          5         18
                    vv
clus                 STAGE IIIC STAGE IV
  21Q LOSS MUTATED            1        0
  21Q LOSS WILD-TYPE         26        7
D75V9, multiclass

Clustering(76) Variable = 22q loss mutation analysis
D76V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    6  3
  22Q LOSS WILD-TYPE 53 52
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 9                105 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 52 
$`22Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JF TCGA-DA-A1I2 TCGA-EB-A41A TCGA-EB-A41B TCGA-EE-A29C 
       28.08        30.87        13.68         0.26         0.10        37.97 
TCGA-EE-A2A6 TCGA-ER-A19D TCGA-FS-A4F0 
        8.94         3.52        53.82 

$`22Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        32.55        70.16        98.76        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.32        24.00         9.30         5.39         4.01         2.86 
TCGA-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        3.88        48.79        35.80        51.12        10.03        39.19 
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-EB-A1NK 
        6.64        19.36         7.00        17.56        14.83         0.53 
TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF 
        0.43         1.35         1.28         1.18         0.30         0.13 
TCGA-EB-A3Y6 TCGA-EB-A42Y TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        0.53         0.20         0.39        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-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-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-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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A 
        6.58         1.71        12.10        10.09         5.95        72.16 
TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 
       24.00         8.81         3.22        10.78         6.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A263 TCGA-GN-A264 
        1.02         0.13        15.35        24.85        15.35        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A 
       84.72        10.09        16.21        15.39         5.59        12.16 
TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       24.00        14.70        12.59 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.10               0.13 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             53.82              98.76 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             13.68              10.26 
[1] "0.1 - 53.8 (13.7)" "0.1 - 98.8 (10.3)"
        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-D9-A3Z4 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-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-D9-A3Z4 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I1         TCGA-DA-A1I2 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IA         TCGA-DA-A1IB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1IC         TCGA-DA-A3F2         TCGA-DA-A3F3 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EB-A1NK 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EB-A24C         TCGA-EB-A24D         TCGA-EB-A3HV 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EB-A3XB         TCGA-EB-A3XC         TCGA-EB-A3XF 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EB-A3Y6         TCGA-EB-A41A         TCGA-EB-A41B 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-EB-A42Y         TCGA-EB-A42Z         TCGA-EE-A17X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A182 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A185         TCGA-EE-A20B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29D         TCGA-EE-A29E 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29M 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29Q 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A0 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A2OS         TCGA-FR-A3R1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZN 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F2 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A4F9         TCGA-FS-A4FC         TCGA-FW-A3I3 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FW-A3R5         TCGA-FW-A3TU         TCGA-GN-A261 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A263         TCGA-GN-A264 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A269         TCGA-GN-A26A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A26C         TCGA-GN-A26D         TCGA-IH-A3EA 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D76V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  22Q LOSS MUTATED                    1             2
  22Q LOSS WILD-TYPE                 26            24
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  22Q LOSS MUTATED                                                                                          5
  22Q LOSS WILD-TYPE                                                                                       32
                    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                                                                                           2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         22Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       26
  PRIMARY TUMOR                                                                                            24
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                     105
D76V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      7    8
  22Q LOSS WILD-TYPE   69  118
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                7                 69
  MALE                  8                118
D76V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      0   15
  22Q LOSS WILD-TYPE    3  184
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 0                  3
  YES               15                184
                    vv
clus                  M0  M1 M1A M1B M1C
  22Q LOSS MUTATED    14   0   0   1   0
  22Q LOSS WILD-TYPE 162   2   2   1   3
D76V6, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  22Q LOSS MUTATED   11  0   1   1  0   0   1   0  1  0
  22Q LOSS WILD-TYPE 99  2   7  16  1   5  13   6 18  5
D76V7, multiclass
D76V8, 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       12       20         9
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  22Q LOSS MUTATED           1         2         0          0          1
  22Q LOSS WILD-TYPE         9        21         9          7         20
                    vv
clus                 STAGE IIIC STAGE IV
  22Q LOSS MUTATED            1        1
  22Q LOSS WILD-TYPE         26        6
D76V9, multiclass

Clustering(77) Variable = Xq loss mutation analysis
D77V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    2  1
  XQ LOSS WILD-TYPE 57 54
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               111 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                54 
$`XQ LOSS MUTATED`
TCGA-D3-A3C6 TCGA-EE-A29H TCGA-GN-A262 
       15.25         4.41        24.85 

$`XQ LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-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-D9-A3Z4 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        2.86         3.88        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-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
       14.83         0.53         0.43         1.35         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y 
        0.30         0.13         0.53         0.26         0.10         0.20 
TCGA-EB-A42Z TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
        0.39        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-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-A2OS TCGA-FR-A3R1 TCGA-FR-A3YN TCGA-FR-A44A 
        6.58         1.71        12.10        10.09         5.95        72.16 
TCGA-FS-A1ZN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC 
       24.00         8.81        53.82         3.22        10.78         6.41 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A263 TCGA-GN-A264 
        0.20         1.02         0.13        15.35        15.35        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A 
       84.72        10.09        16.21        15.39         5.59        12.16 
TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
       24.00        14.70        12.59 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             4.41              0.10 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            24.85             98.76 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            15.25             10.26 
[1] "4.4 - 24.9 (15.2)" "0.1 - 98.8 (10.3)"
       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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"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-D9-A3Z4        TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EB-A1NK        TCGA-EB-A24C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A41A        TCGA-EB-A41B 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EB-A42Y        TCGA-EB-A42Z        TCGA-EE-A17X        TCGA-EE-A17Z 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-EE-A29L        TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FR-A3R1        TCGA-FR-A3YN        TCGA-FR-A44A 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A1ZN        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-A263 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A269        TCGA-GN-A26A        TCGA-GN-A26C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A26D        TCGA-IH-A3EA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D77V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  XQ LOSS MUTATED                    1             0
  XQ LOSS WILD-TYPE                 26            26
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  XQ LOSS MUTATED                                                                                          1
  XQ LOSS WILD-TYPE                                                                                       36
                   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)               1
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         XQ LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      26
  PRIMARY TUMOR                                                                                           26
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                36
  REGIONAL LYMPH NODE                                                                                    109
D77V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4    1
  XQ LOSS WILD-TYPE   72  125
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               4                72
  MALE                 1               125
D77V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    5
  XQ LOSS WILD-TYPE    3  194
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                0                 3
  YES               5               194
                   vv
clus                 M0  M1 M1A M1B M1C
  XQ LOSS MUTATED     4   0   0   0   0
  XQ LOSS WILD-TYPE 172   2   2   2   3
D77V6, multiclass
                   vv
clus                 N0  N1 N1A N1B  N2 N2A N2B N2C  N3  NX
  XQ LOSS MUTATED     4   0   0   0   0   0   0   0   0   0
  XQ LOSS WILD-TYPE 106   2   8  17   1   5  14   6  19   5
D77V7, multiclass
D77V8, 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       14       20         9
                   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        23         9          7         21
                   vv
clus                STAGE IIIC STAGE IV
  XQ LOSS MUTATED            0        0
  XQ LOSS WILD-TYPE         27        7
D77V9, multiclass
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
               "PRIMARY.SITE.OF.DISEASE" 
                                      V4 
                                "GENDER" 
                                      V5 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V6 
                    "DISTANT.METASTASIS" 
                                      V7 
                 "LYMPH.NODE.METASTASIS" 
                                      V8 
                       "TUMOR.STAGECODE" 
                                      V9 
                 "NEOPLASM.DISEASESTAGE" 
> q(save="no")
