
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/19/CNV2ClinicalAnalysis_nozzle_onlysig_arm.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/19/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/SKCM-Regional_LN/3164429/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-Regional_LN/3215666/SKCM-Regional_LN.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-Regional_LN", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"                  "-oT=SKCM-Regional_LN"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=116, in cluster file=112, common to both=112
[1] "Reduce the number of clustering variables from 80 to 72."
[1]  72 112
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               12               100 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               12               100 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               33                79 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               33                79 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10               102 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10               102 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                9               103 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                9               103 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                7               105 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                7               105 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               104 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               104 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10               102 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10               102 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10               102 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10               102 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               12               100 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               12               100 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5               107 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5               107 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               35                77 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               35                77 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8               104 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8               104 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               44                68 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               44                68 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               44                68 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               44                68 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               18                94 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               18                94 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               31                81 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               31                81 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               108 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               108 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                104 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                104 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                107 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                107 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                10                102 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                10                102 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                108 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                108 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                 97 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                 97 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 9                103 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 9                103 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                16                 96 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                16                 96 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                106 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                106 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                106 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                106 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                104 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                104 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                15                 97 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                15                 97 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                14                 98 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                14                 98 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                106 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                106 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 8                104 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 8                104 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                103 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                103 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                31                 81 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                31                 81 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                39                 73 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                39                 73 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                11                101 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                11                101 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                24                 88 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                24                 88 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                8               104 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                8               104 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               12               100 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               12               100 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               11               101 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               11               101 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5               107 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5               107 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                8               104 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                8               104 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9               103 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9               103 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10               102 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10               102 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               14                98 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               14                98 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               24                88 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               24                88 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                9               103 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                9               103 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               40                72 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               40                72 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               14                98 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               14                98 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               109 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               109 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               57                55 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               57                55 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               42                70 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               42                70 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                45                 67 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                45                 67 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                49                 63 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                49                 63 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                26                 86 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                26                 86 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                30                 82 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                30                 82 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                107 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                107 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                104 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                104 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                17                 95 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                17                 95 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                25                 87 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                25                 87 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                105 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                105 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 8                104 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 8                104 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                16                 96 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                16                 96 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                28                 84 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                28                 84 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                13                 99 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                13                 99 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                18                 94 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                18                 94 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                18                 94 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                18                 94 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                12                100 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                12                100 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                100 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                100 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                109 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                109 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 97 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 97 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 7                105 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 7                105 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               109 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               109 
[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 112 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
          NA           NA         3004           NA           NA           NA 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
          NA           NA           NA           NA           NA           NA 
TCGA-D3-A3CF TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
          NA           NA           NA           NA          122           87 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 
        1484           NA         1555           NA          680           NA 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
         534          451           NA           NA           NA           NA 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
          NA          156         1155           NA         1175          134 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
          NA           NA          366          269          304          197 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
          NA           NA          769          727          272           NA 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GL TCGA-EE-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-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AH TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
          NA           NA           NA           NA           NA         1303 
TCGA-ER-A19O TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1Z4 
          NA         2386          181         2195           NA           NA 
TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GN-A264 
          NA           NA          328           31           NA           NA 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
        2577           NA           NA          447 
Variable 1:'AGE':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=57,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=4,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "GENDER"                "DISTANT.METASTASIS"   
[4] "LYMPH.NODE.METASTASIS" "TUMOR.STAGECODE"       "NEOPLASM.DISEASESTAGE"
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
 T0  T1 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 T4A T4B TIS  TX 
  4   4  10   3  12  12   4   3  13   7   1   5  15   1   8 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 112 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=55, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=4, 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    3  3
  1P GAIN WILD-TYPE 24 29
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6                53 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3                29 
$`1P GAIN MUTATED`
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FR-A3YN 
       11.15        38.63         1.08        23.90        11.11         5.95 

$`1P 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-A3CE 
        8.38        21.14        11.41         6.35        15.25        13.32 
TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       24.00         4.01         2.86        48.79        35.80        51.12 
TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
       13.68        22.36         7.00        17.56        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C 
        6.31         1.12        12.20         4.27         5.13        37.97 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        4.41         9.47        12.03         8.84         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A19L 
        8.09        11.31        25.28         8.94         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 
       28.64        42.84        78.44        72.16        10.78         1.02 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       31.33        84.72        16.21        15.39        14.70 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.08              1.02 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            38.63             98.76 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            11.13             13.32 
[1] "1.1 - 38.6 (11.1)" "1.0 - 98.8 (13.3)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "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-FR-A3YN        TCGA-FR-A44A 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "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-FR-A3YN        TCGA-FR-A44A 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "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-FR-A3YN        TCGA-FR-A44A 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    9
  1P GAIN WILD-TYPE   32   68
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               3                32
  MALE                 9                68
                   vv
clus                M0 M1 M1B M1C
  1P GAIN MUTATED   12  0   0   0
  1P GAIN WILD-TYPE 86  1   2   1
D1V4, multiclass
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               12                86
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  1P GAIN MUTATED    6  0   0   3  0   2   0   0  1  0
  1P GAIN WILD-TYPE 55  1   3   7  1   1   8   1 12  2
D1V5, multiclass
D1V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1P GAIN MUTATED             0       1        1        2        1         0
  1P GAIN WILD-TYPE           1      14        6        9       12         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1P GAIN MUTATED           0         0         0          1          2
  1P GAIN WILD-TYPE         5         2         4          2          8
                   vv
clus                STAGE IIIC STAGE IV
  1P GAIN MUTATED            2        0
  1P GAIN WILD-TYPE         16        3
D1V7, multiclass

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   10 10
  1Q GAIN WILD-TYPE 17 22
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               20                39 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               10                22 
$`1Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J8 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D9-A3Z3 TCGA-DA-A3F3 
       16.47         8.38        11.41        13.32         2.86         7.00 
TCGA-EE-A17Z TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S 
        6.31        11.15        38.63         1.08         8.84         9.99 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-FR-A3YN TCGA-FR-A44A 
       25.28        23.90         8.94        11.11         5.95        72.16 
TCGA-GN-A267 TCGA-GN-A26D 
       16.21        14.70 

$`1Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J9 
       32.55        98.76        28.08        22.55        10.26        21.14 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HW 
        6.35        15.25        24.00         4.01        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
       51.12        13.68        22.36        17.56        14.83        11.57 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29H 
        1.12        12.20         4.27         5.13        37.97         4.41 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-ER-A19J 
        9.47        12.03         6.48         8.09        11.31         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FS-A4F9 TCGA-FW-A3R5 
       12.99        28.64        42.84        78.44        10.78         1.02 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
       31.33        84.72        15.39 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             1.08              1.02 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            72.16             98.76 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            11.13             14.83 
[1] "1.1 - 72.2 (11.1)" "1.0 - 98.8 (14.8)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "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-FR-A3YN        TCGA-FR-A44A 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "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-FR-A3YN        TCGA-FR-A44A 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "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-FR-A3YN        TCGA-FR-A44A 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
[1] "hr=" "1.3"
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      8   25
  1Q GAIN WILD-TYPE   27   52
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               8                27
  MALE                25                52
                   vv
clus                M0 M1 M1B M1C
  1Q GAIN MUTATED   30  0   0   0
  1Q GAIN WILD-TYPE 68  1   2   1
D2V4, multiclass
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0               30                68
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  1Q GAIN MUTATED   18  0   1   7  0   2   1   0  2  0
  1Q GAIN WILD-TYPE 43  1   2   3  1   1   7   1 11  2
D2V5, multiclass
D2V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1Q GAIN MUTATED             0       2        3        5        4         1
  1Q GAIN WILD-TYPE           1      13        4        6        9         4
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1Q GAIN MUTATED           1         1         1          2          4
  1Q GAIN WILD-TYPE         4         1         3          1          6
                   vv
clus                STAGE IIIC STAGE IV
  1Q GAIN MUTATED            5        0
  1Q GAIN WILD-TYPE         13        3
D2V7, multiclass

Clustering(3) Variable = 2p gain mutation analysis
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    4  5
  2P GAIN WILD-TYPE 23 27
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                9                50 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                5                27 
$`2P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29R 
       16.47        22.55        11.41        11.15         1.08         8.84 
TCGA-ER-A19N TCGA-FR-A3YN TCGA-FR-A44A 
       42.84         5.95        72.16 

$`2P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        10.26         8.38        21.14 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 
        6.35        15.25        13.32        24.00         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 
       48.79        35.80        51.12        13.68        22.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N 
        4.27         5.13        37.97        38.63         4.41         9.47 
TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       12.03         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       23.90         8.94        11.11         4.18        12.99        28.64 
TCGA-ER-A1A1 TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       78.44        10.78         1.02        31.33        84.72        16.21 
TCGA-GN-A268 TCGA-GN-A26D 
       15.39        14.70 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1.08              1.02 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            72.16             98.76 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           11.410            13.155 
[1] "1.1 - 72.2 (11.4)" "1.0 - 98.8 (13.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D3V2, continuous
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3    7
  2P GAIN WILD-TYPE   32   70
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               3                32
  MALE                 7                70
                   vv
clus                M0 M1 M1B M1C
  2P GAIN MUTATED    9  0   0   0
  2P GAIN WILD-TYPE 89  1   2   1
D3V4, multiclass
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0                9                89
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  2P GAIN MUTATED    3  0   0   3  0   1   0   0  2  0
  2P GAIN WILD-TYPE 58  1   3   7  1   2   8   1 11  2
D3V5, multiclass
D3V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2P GAIN MUTATED             0       0        0        1        1         1
  2P GAIN WILD-TYPE           1      15        7       10       12         4
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  2P GAIN MUTATED           0         0         0          0          1
  2P GAIN WILD-TYPE         5         2         4          3          9
                   vv
clus                STAGE IIIC STAGE IV
  2P GAIN MUTATED            5        0
  2P GAIN WILD-TYPE         13        3
D3V7, multiclass

Clustering(4) Variable = 2q gain mutation analysis
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    4  4
  2Q GAIN WILD-TYPE 23 28
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                8                51 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                4                28 
$`2Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-EE-A29L TCGA-EE-A29R TCGA-ER-A19N 
       16.47        22.55        11.41         1.08         8.84        42.84 
TCGA-FR-A3YN TCGA-FR-A44A 
        5.95        72.16 

$`2Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        10.26         8.38        21.14 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 
        6.35        15.25        13.32        24.00         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 
       48.79        35.80        51.12        13.68        22.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        4.27         5.13        37.97        11.15        38.63         4.41 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        9.47        12.03         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       25.28        23.90         8.94        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A1A1 TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 
       28.64        78.44        10.78         1.02        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       16.21        15.39        14.70 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.08              1.02 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            72.16             98.76 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            13.94             12.99 
[1] "1.1 - 72.2 (13.9)" "1.0 - 98.8 (13.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3    6
  2Q GAIN WILD-TYPE   32   71
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               3                32
  MALE                 6                71
                   vv
clus                M0 M1 M1B M1C
  2Q GAIN MUTATED    8  0   0   0
  2Q GAIN WILD-TYPE 90  1   2   1
D4V4, multiclass
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0                8                90
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  2Q GAIN MUTATED    3  0   0   2  0   1   0   0  2  0
  2Q GAIN WILD-TYPE 58  1   3   8  1   2   8   1 11  2
D4V5, multiclass
D4V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2Q GAIN MUTATED             0       0        0        1        1         1
  2Q GAIN WILD-TYPE           1      15        7       10       12         4
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  2Q GAIN MUTATED           0         0         0          0          1
  2Q GAIN WILD-TYPE         5         2         4          3          9
                   vv
clus                STAGE IIIC STAGE IV
  2Q GAIN MUTATED            4        0
  2Q GAIN WILD-TYPE         14        3
D4V7, multiclass

Clustering(5) Variable = 3p gain mutation analysis
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    3  3
  3P GAIN WILD-TYPE 24 29
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                6                53 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                29 
$`3P GAIN MUTATED`
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29T TCGA-GN-A264 
        7.00        17.56         1.08         8.84         6.48        31.33 

$`3P 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-A3CE 
        8.38        21.14        11.41         6.35        15.25        13.32 
TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       24.00         4.01         2.86        48.79        35.80        51.12 
TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       13.68        22.36        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       12.20         4.27         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 
        4.41         9.47        12.03         9.99         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       25.28        23.90         8.94        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 
       28.64        42.84        78.44         5.95        72.16        10.78 
TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
        1.02        84.72        16.21        15.39        14.70 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             1.08              1.02 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            31.33             98.76 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             7.92             13.32 
[1] "1.1 - 31.3 (7.9)"  "1.0 - 98.8 (13.3)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3    4
  3P GAIN WILD-TYPE   32   73
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               3                32
  MALE                 4                73
                   vv
clus                M0 M1 M1B M1C
  3P GAIN MUTATED    6  0   0   0
  3P GAIN WILD-TYPE 92  1   2   1
D5V4, multiclass
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0                6                92
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  3P GAIN MUTATED    1  0   0   1  0   0   1   0  2  1
  3P GAIN WILD-TYPE 60  1   3   9  1   3   7   1 11  1
D5V5, multiclass
D5V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3P GAIN MUTATED             0       0        1        0        0         0
  3P GAIN WILD-TYPE           1      15        6       11       13         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  3P GAIN MUTATED           0         0         0          0          1
  3P GAIN WILD-TYPE         5         2         4          3          9
                   vv
clus                STAGE IIIC STAGE IV
  3P GAIN MUTATED            3        0
  3P GAIN WILD-TYPE         15        3
D5V7, multiclass

Clustering(6) Variable = 3q gain mutation analysis
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    4  2
  3Q GAIN WILD-TYPE 23 30
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                6                53 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                30 
$`3Q GAIN MUTATED`
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A20F TCGA-EE-A29R TCGA-EE-A29T TCGA-ER-A19M 
        7.00        17.56         5.13         8.84         6.48        28.64 

$`3Q 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-A3CE 
        8.38        21.14        11.41         6.35        15.25        13.32 
TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       24.00         4.01         2.86        48.79        35.80        51.12 
TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       13.68        22.36        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       12.20         4.27        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 
        1.08         9.47        12.03         9.99         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       25.28        23.90         8.94        11.11         4.18        12.99 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 
       42.84        78.44         5.95        72.16        10.78         1.02 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       31.33        84.72        16.21        15.39        14.70 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             5.13              1.02 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            28.64             98.76 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             7.92             13.32 
[1] "5.1 - 28.6 (7.9)"  "1.0 - 98.8 (13.3)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    5
  3Q GAIN WILD-TYPE   32   72
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               3                32
  MALE                 5                72
                   vv
clus                M0 M1 M1B M1C
  3Q GAIN MUTATED    8  0   0   0
  3Q GAIN WILD-TYPE 90  1   2   1
D6V4, multiclass
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0                8                90
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  3Q GAIN MUTATED    4  0   0   1  0   0   1   0  1  1
  3Q GAIN WILD-TYPE 57  1   3   9  1   3   7   1 12  1
D6V5, multiclass
D6V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3Q GAIN MUTATED             0       0        1        1        2         0
  3Q GAIN WILD-TYPE           1      15        6       10       11         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  3Q GAIN MUTATED           0         0         0          0          1
  3Q GAIN WILD-TYPE         5         2         4          3          9
                   vv
clus                STAGE IIIC STAGE IV
  3Q GAIN MUTATED            2        0
  3Q GAIN WILD-TYPE         16        3
D6V7, multiclass

Clustering(7) Variable = 4p gain mutation analysis
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    5  2
  4P GAIN WILD-TYPE 22 30
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                7                52 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                30 
$`4P GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A1HV TCGA-DA-A3F5 TCGA-EE-A29P TCGA-FR-A3YN TCGA-GN-A264 
       13.32        48.79        17.56        12.03         5.95        31.33 
TCGA-GN-A26D 
       14.70 

$`4P 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-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB 
        4.01         2.86        35.80        51.12        13.68        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
        7.00        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        4.27         5.13        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
        1.08         9.47         8.84         9.99         6.48         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J 
       11.31        25.28        23.90         8.94        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A44A TCGA-FS-A4F9 
       12.99        28.64        42.84        78.44        72.16        10.78 
TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.02        84.72        16.21        15.39 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             5.95              1.02 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            48.79             98.76 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           14.700            11.885 
[1] "6.0 - 48.8 (14.7)" "1.0 - 98.8 (11.9)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
[1] "hr=" "2.4"
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      5    5
  4P GAIN WILD-TYPE   30   72
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               5                30
  MALE                 5                72
                   vv
clus                M0 M1 M1B M1C
  4P GAIN MUTATED    8  0   0   0
  4P GAIN WILD-TYPE 90  1   2   1
D7V4, multiclass
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0                8                90
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  4P GAIN MUTATED    5  0   1   1  0   0   1   0  1  0
  4P GAIN WILD-TYPE 56  1   2   9  1   3   7   1 12  2
D7V5, multiclass
D7V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4P GAIN MUTATED             0       1        1        1        0         0
  4P GAIN WILD-TYPE           1      14        6       10       13         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4P GAIN MUTATED           0         2         1          1          1
  4P GAIN WILD-TYPE         5         0         3          2          9
                   vv
clus                STAGE IIIC STAGE IV
  4P GAIN MUTATED            1        0
  4P GAIN WILD-TYPE         17        3
D7V7, multiclass

Clustering(8) Variable = 4q gain mutation analysis
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    5  3
  4Q GAIN WILD-TYPE 22 29
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8                51 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                29 
$`4Q GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A1HV TCGA-DA-A3F5 TCGA-EE-A29D TCGA-EE-A29P TCGA-FR-A3YN 
       13.32        48.79        17.56        11.15        12.03         5.95 
TCGA-GN-A264 TCGA-GN-A26D 
       31.33        14.70 

$`4Q 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-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB 
        4.01         2.86        35.80        51.12        13.68        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
        7.00        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        4.27         5.13        37.97        38.63         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        9.47         8.84         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       25.28        23.90         8.94        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 
       28.64        42.84        78.44        72.16        10.78         1.02 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       84.72        16.21        15.39 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             5.95              1.02 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            48.79             98.76 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            14.01             12.20 
[1] "6.0 - 48.8 (14.0)" "1.0 - 98.8 (12.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
[1] "hr=" "1.7"
D8V2, continuous
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    6
  4Q GAIN WILD-TYPE   31   71
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               4                31
  MALE                 6                71
                   vv
clus                M0 M1 M1B M1C
  4Q GAIN MUTATED    7  0   0   0
  4Q GAIN WILD-TYPE 91  1   2   1
D8V4, multiclass
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0                7                91
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  4Q GAIN MUTATED    3  0   1   2  0   0   1   0  1  0
  4Q GAIN WILD-TYPE 58  1   2   8  1   3   7   1 12  2
D8V5, multiclass
D8V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4Q GAIN MUTATED             0       0        0        1        0         0
  4Q GAIN WILD-TYPE           1      15        7       10       13         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4Q GAIN MUTATED           0         2         1          1          1
  4Q GAIN WILD-TYPE         5         0         3          2          9
                   vv
clus                STAGE IIIC STAGE IV
  4Q GAIN MUTATED            2        0
  4Q GAIN WILD-TYPE         16        3
D8V7, multiclass

Clustering(9) Variable = 5p gain mutation analysis
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    1  4
  5P GAIN WILD-TYPE 26 28
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                5                54 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                4                28 
$`5P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A2JK TCGA-EE-A29T TCGA-EE-A2A0 TCGA-ER-A19M 
       32.55         6.35         6.48        11.31        28.64 

$`5P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 
       21.14        11.41        15.25        13.32        24.00         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB 
        2.86        48.79        35.80        51.12        13.68        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        7.00        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       12.20         4.27         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
        4.41         1.08         9.47        12.03         8.84         9.99 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J 
        8.09        25.28        23.90         8.94        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 
       12.99        42.84        78.44         5.95        72.16        10.78 
TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
        1.02        31.33        84.72        16.21        15.39        14.70 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             6.35              1.02 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            32.55             98.76 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           11.310            13.155 
[1] "6.3 - 32.5 (11.3)" "1.0 - 98.8 (13.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "5P GAIN MUTATED" "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-FR-A3YN        TCGA-FR-A44A 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "5P GAIN MUTATED" "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-FR-A3YN        TCGA-FR-A44A 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "5P GAIN MUTATED" "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-FR-A3YN        TCGA-FR-A44A 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4    8
  5P GAIN WILD-TYPE   31   69
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               4                31
  MALE                 8                69
                   vv
clus                M0 M1 M1B M1C
  5P GAIN MUTATED   11  0   1   0
  5P GAIN WILD-TYPE 87  1   1   1
D9V4, multiclass
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0               11                87
  M1                0                 1
  M1B               1                 1
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  5P GAIN MUTATED    7  0   0   1  0   1   1   0  1  1
  5P GAIN WILD-TYPE 54  1   3   9  1   2   7   1 12  1
D9V5, multiclass
D9V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5P GAIN MUTATED             1       2        1        1        1         1
  5P GAIN WILD-TYPE           0      13        6       10       12         4
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5P GAIN MUTATED           0         0         0          0          1
  5P GAIN WILD-TYPE         5         2         4          3          9
                   vv
clus                STAGE IIIC STAGE IV
  5P GAIN MUTATED            1        0
  5P GAIN WILD-TYPE         17        3
D9V7, multiclass

Clustering(10) Variable = 5q gain mutation analysis
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN WILD-TYPE 27 32
5Q GAIN WILD-TYPE 
               59 
[1] 32
$`5Q 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-A3CE 
        8.38        21.14        11.41         6.35        15.25        13.32 
TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       24.00         4.01         2.86        48.79        35.80        51.12 
TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
       13.68        22.36         7.00        17.56        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C 
        6.31         1.12        12.20         4.27         5.13        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       11.15        38.63         4.41         1.08         9.47        12.03 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       23.90         8.94        11.11         4.18        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 
       42.84        78.44         5.95        72.16        10.78         1.02 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       31.33        84.72        16.21        15.39        14.70 

5Q GAIN WILD-TYPE 
             1.02 
5Q GAIN WILD-TYPE 
            98.76 
5Q GAIN WILD-TYPE 
            12.99 
[1] "1.0 - 98.8 (13.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    3
  5Q GAIN WILD-TYPE   33   74
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               2                33
  MALE                 3                74
                   vv
clus                M0 M1 M1B M1C
  5Q GAIN MUTATED    5  0   0   0
  5Q GAIN WILD-TYPE 93  1   2   1
D10V4, multiclass
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0                5                93
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  5Q GAIN MUTATED    4  0   0   0  0   1   0   0  0  0
  5Q GAIN WILD-TYPE 57  1   3  10  1   2   8   1 13  2
D10V5, multiclass
D10V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5Q GAIN MUTATED             0       1        1        0        1         1
  5Q GAIN WILD-TYPE           1      14        6       11       12         4
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5Q GAIN MUTATED           0         0         0          0          0
  5Q GAIN WILD-TYPE         5         2         4          3         10
                   vv
clus                STAGE IIIC STAGE IV
  5Q GAIN MUTATED            0        0
  5Q GAIN WILD-TYPE         18        3
D10V7, multiclass

Clustering(11) Variable = 6p gain mutation analysis
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    7 10
  6P GAIN WILD-TYPE 20 22
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               17                42 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               10                22 
$`6P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A3C6 TCGA-DA-A1HV TCGA-DA-A1I2 
       16.47        98.76        21.14        15.25        48.79        13.68 
TCGA-DA-A3F3 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A29P TCGA-EE-A29R 
        7.00         6.31         1.12         4.27        12.03         8.84 
TCGA-EE-A29S TCGA-ER-A19M TCGA-ER-A19N TCGA-GN-A264 TCGA-GN-A26D 
        9.99        28.64        42.84        31.33        14.70 

$`6P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JD 
       32.55        28.08        22.55        10.26         8.38        11.41 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW 
        6.35        13.32        24.00         4.01         2.86        35.80 
TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A183 
       51.12        22.36        17.56        14.83        11.57        12.20 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        5.13        37.97        11.15        38.63         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.47         6.48         8.09        11.31        25.28        23.90 
TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A1A1 TCGA-FR-A3YN 
        8.94        11.11         4.18        12.99        78.44         5.95 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       72.16        10.78         1.02        84.72        16.21        15.39 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             1.12              1.02 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            98.76             84.72 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           14.700            11.885 
[1] "1.1 - 98.8 (14.7)" "1.0 - 84.7 (11.9)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "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 WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-FR-A3YN        TCGA-FR-A44A 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "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 WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-FR-A3YN        TCGA-FR-A44A 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "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 WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-FR-A3YN        TCGA-FR-A44A 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
[1] "hr=" "1"  
D11V2, continuous
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     16   19
  6P GAIN WILD-TYPE   19   58
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              16                19
  MALE                19                58
                   vv
clus                M0 M1 M1B M1C
  6P GAIN MUTATED   30  0   0   0
  6P GAIN WILD-TYPE 68  1   2   1
D11V4, multiclass
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               30                68
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  6P GAIN MUTATED   20  0   1   2  0   2   3   0  3  0
  6P GAIN WILD-TYPE 41  1   2   8  1   1   5   1 10  2
D11V5, multiclass
D11V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6P GAIN MUTATED             0       4        2        4        4         2
  6P GAIN WILD-TYPE           1      11        5        7        9         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6P GAIN MUTATED           2         2         0          2          3
  6P GAIN WILD-TYPE         3         0         4          1          7
                   vv
clus                STAGE IIIC STAGE IV
  6P GAIN MUTATED            5        0
  6P GAIN WILD-TYPE         13        3
D11V7, multiclass

Clustering(12) Variable = 6q gain mutation analysis
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    2  1
  6Q GAIN WILD-TYPE 25 31
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3                56 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                31 
$`6Q GAIN MUTATED`
TCGA-D3-A1Q7 TCGA-EE-A29R TCGA-ER-A19M 
       98.76         8.84        28.64 

$`6Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        32.55        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       22.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
        1.12        12.20         4.27         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S 
       38.63         4.41         1.08         9.47        12.03         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        6.48         8.09        11.31        25.28        23.90         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN 
       11.11         4.18        12.99        42.84        78.44         5.95 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       72.16        10.78         1.02        31.33        84.72        16.21 
TCGA-GN-A268 TCGA-GN-A26D 
       15.39        14.70 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             8.84              1.02 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            98.76             84.72 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           28.640            12.595 
[1] "8.8 - 98.8 (28.6)" "1.0 - 84.7 (12.6)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
[1] "hr=" "2.6"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    5
  6Q GAIN WILD-TYPE   32   72
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               3                32
  MALE                 5                72
                   vv
clus                M0 M1 M1B M1C
  6Q GAIN MUTATED    8  0   0   0
  6Q GAIN WILD-TYPE 90  1   2   1
D12V4, multiclass
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0                8                90
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  6Q GAIN MUTATED    7  0   0   1  0   0   0   0  0  0
  6Q GAIN WILD-TYPE 54  1   3   9  1   3   8   1 13  2
D12V5, multiclass
D12V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6Q GAIN MUTATED             0       0        1        3        1         1
  6Q GAIN WILD-TYPE           1      15        6        8       12         4
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6Q GAIN MUTATED           1         0         0          0          0
  6Q GAIN WILD-TYPE         4         2         4          3         10
                   vv
clus                STAGE IIIC STAGE IV
  6Q GAIN MUTATED            1        0
  6Q GAIN WILD-TYPE         17        3
D12V7, multiclass

Clustering(13) Variable = 7p gain mutation analysis
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   10 12
  7P GAIN WILD-TYPE 17 20
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               22                37 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               12                20 
$`7P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D9-A3Z3 TCGA-DA-A1HV 
       16.47        32.55        22.55        11.41         2.86        48.79 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       51.12        13.68         1.12        37.97        11.15        38.63 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-ER-A19J 
        9.47        12.03         6.48        11.31         8.94         4.18 
TCGA-FR-A3YN TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26D 
        5.95        31.33        16.21        14.70 

$`7P GAIN WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JK 
       98.76        28.08        10.26         8.38        21.14         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1HW TCGA-DA-A1IB 
       15.25        13.32        24.00         4.01        35.80        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 
        7.00        17.56        14.83        11.57         6.31        12.20 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S 
        4.27         5.13         4.41         1.08         8.84         9.99 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M 
        8.09        25.28        23.90        11.11        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A265 
       42.84        78.44        72.16        10.78         1.02        84.72 
TCGA-GN-A268 
       15.39 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             1.12              1.02 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            51.12             98.76 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           12.855            12.990 
[1] "1.1 - 51.1 (12.9)" "1.0 - 98.8 (13.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       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-FR-A3YN        TCGA-FR-A44A 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       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-FR-A3YN        TCGA-FR-A44A 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       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-FR-A3YN        TCGA-FR-A44A 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
[1] "hr=" "1.1"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     14   30
  7P GAIN WILD-TYPE   21   47
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              14                21
  MALE                30                47
                   vv
clus                M0 M1 M1B M1C
  7P GAIN MUTATED   38  1   0   1
  7P GAIN WILD-TYPE 60  0   2   0
D13V4, multiclass
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0               38                60
  M1                1                 0
  M1B               0                 2
  M1C               1                 0
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  7P GAIN MUTATED   23  0   2   6  0   2   2   1  3  2
  7P GAIN WILD-TYPE 38  1   1   4  1   1   6   0 10  0
D13V5, multiclass
D13V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  7P GAIN MUTATED             1       5        4        2        6         2
  7P GAIN WILD-TYPE           0      10        3        9        7         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  7P GAIN MUTATED           0         2         0          3          5
  7P GAIN WILD-TYPE         5         0         4          0          5
                   vv
clus                STAGE IIIC STAGE IV
  7P GAIN MUTATED            6        2
  7P GAIN WILD-TYPE         12        1
D13V7, multiclass

Clustering(14) Variable = 7q gain mutation analysis
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   12 12
  7Q GAIN WILD-TYPE 15 20
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               24                35 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               12                20 
$`7Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D9-A3Z3 TCGA-DA-A1HV 
       16.47        32.55        22.55        11.41         2.86        48.79 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A183 
       51.12        13.68        17.56        14.83         1.12        12.20 
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-FR-A3YN TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26D 
        8.94         4.18         5.95        31.33        16.21        14.70 

$`7Q GAIN WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JK 
       98.76        28.08        10.26         8.38        21.14         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1HW TCGA-DA-A1IB 
       15.25        13.32        24.00         4.01        35.80        22.36 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D 
        7.00        11.57         6.31         4.27         5.13        11.15 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A1 
        4.41         1.08         8.84         9.99         8.09        25.28 
TCGA-EE-A2A2 TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       23.90        11.11        12.99        28.64        42.84        78.44 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A268 
       72.16        10.78         1.02        84.72        15.39 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             1.12              1.02 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            51.12             98.76 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            14.19             11.57 
[1] "1.1 - 51.1 (14.2)" "1.0 - 98.8 (11.6)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       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-FR-A3YN        TCGA-FR-A44A 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       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-FR-A3YN        TCGA-FR-A44A 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       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-FR-A3YN        TCGA-FR-A44A 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
[1] "hr=" "1.3"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     14   30
  7Q GAIN WILD-TYPE   21   47
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              14                21
  MALE                30                47
                   vv
clus                M0 M1 M1B M1C
  7Q GAIN MUTATED   39  1   0   1
  7Q GAIN WILD-TYPE 59  0   2   0
D14V4, multiclass
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0               39                59
  M1                1                 0
  M1B               0                 2
  M1C               1                 0
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  7Q GAIN MUTATED   23  0   2   5  0   2   3   1  4  2
  7Q GAIN WILD-TYPE 38  1   1   5  1   1   5   0  9  0
D14V5, multiclass
D14V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  7Q GAIN MUTATED             1       5        3        2        7         2
  7Q GAIN WILD-TYPE           0      10        4        9        6         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  7Q GAIN MUTATED           0         2         0          3          6
  7Q GAIN WILD-TYPE         5         0         4          0          4
                   vv
clus                STAGE IIIC STAGE IV
  7Q GAIN MUTATED            6        2
  7Q GAIN WILD-TYPE         12        1
D14V7, multiclass

Clustering(15) Variable = 8p gain mutation analysis
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    5  7
  8P GAIN WILD-TYPE 22 25
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12                47 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                25 
$`8P GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A3F5 TCGA-EE-A181 TCGA-EE-A29R 
       13.32        51.12        13.68        17.56         1.12         8.84 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A26D 
        4.18        12.99        28.64        42.84        16.21        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-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1IB TCGA-DA-A3F3 
        4.01         2.86        48.79        35.80        22.36         7.00 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
       14.83        11.57         6.31        12.20         4.27         5.13 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       37.97        11.15        38.63         4.41         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       12.03         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A 
       23.90         8.94        11.11        78.44         5.95        72.16 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
       10.78         1.02        31.33        84.72        15.39 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             1.12              1.02 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            51.12             98.76 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            14.19             11.57 
[1] "1.1 - 51.1 (14.2)" "1.0 - 98.8 (11.6)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
[1] "hr=" "1"  
D15V2, continuous
D15V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4   14
  8P GAIN WILD-TYPE   31   63
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               4                31
  MALE                14                63
                   vv
clus                M0 M1 M1B M1C
  8P GAIN MUTATED   13  1   0   0
  8P GAIN WILD-TYPE 85  0   2   1
D15V4, multiclass
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               13                85
  M1                1                 0
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  8P GAIN MUTATED    7  0   1   3  0   0   1   0  3  0
  8P GAIN WILD-TYPE 54  1   2   7  1   3   7   1 10  2
D15V5, multiclass
D15V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8P GAIN MUTATED             0       1        0        2        2         1
  8P GAIN WILD-TYPE           1      14        7        9       11         4
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8P GAIN MUTATED           0         1         1          1          0
  8P GAIN WILD-TYPE         5         1         3          2         10
                   vv
clus                STAGE IIIC STAGE IV
  8P GAIN MUTATED            5        1
  8P GAIN WILD-TYPE         13        2
D15V7, multiclass

Clustering(16) Variable = 8q gain mutation analysis
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED    7 12
  8Q GAIN WILD-TYPE 20 20
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               19                40 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               12                20 
$`8Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A3CE TCGA-DA-A1HY TCGA-DA-A1I2 
       16.47        22.55        10.26        13.32        51.12        13.68 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29R 
        7.00        17.56         6.31         1.12        38.63         8.84 
TCGA-EE-A29T TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-GN-A267 
        6.48         4.18        12.99        28.64        42.84        16.21 
TCGA-GN-A26D 
       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-A1IB TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A185 
       35.80        22.36        14.83        11.57        12.20         4.27 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
        5.13        37.97        11.15         4.41         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
       12.03         9.99         8.09        11.31        25.28        23.90 
TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 
        8.94        11.11        78.44         5.95        72.16        10.78 
TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
        1.02        31.33        84.72        15.39 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             1.12              1.02 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            51.12             98.76 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            13.68             11.80 
[1] "1.1 - 51.1 (13.7)" "1.0 - 98.8 (11.8)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "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-FR-A3YN        TCGA-FR-A44A 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "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-FR-A3YN        TCGA-FR-A44A 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "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-FR-A3YN        TCGA-FR-A44A 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
[1] "hr=" "1.3"
D16V2, continuous
D16V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      7   24
  8Q GAIN WILD-TYPE   28   53
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               7                28
  MALE                24                53
                   vv
clus                M0 M1 M1B M1C
  8Q GAIN MUTATED   25  1   0   0
  8Q GAIN WILD-TYPE 73  0   2   1
D16V4, multiclass
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0               25                73
  M1                1                 0
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  8Q GAIN MUTATED   13  0   1   4  0   2   2   0  4  1
  8Q GAIN WILD-TYPE 48  1   2   6  1   1   6   1  9  1
D16V5, multiclass
D16V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8Q GAIN MUTATED             0       3        0        3        3         1
  8Q GAIN WILD-TYPE           1      12        7        8       10         4
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8Q GAIN MUTATED           2         1         1          1          3
  8Q GAIN WILD-TYPE         3         1         3          2          7
                   vv
clus                STAGE IIIC STAGE IV
  8Q GAIN MUTATED            6        1
  8Q GAIN WILD-TYPE         12        2
D16V7, multiclass

Clustering(17) Variable = 9q gain mutation analysis
D17V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    1  1
  9Q GAIN WILD-TYPE 26 31
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                57 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                31 
$`9Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-FR-A44A 
       22.55        72.16 

$`9Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        32.55        98.76        28.08        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       22.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
        1.12        12.20         4.27         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       38.63         4.41         1.08         9.47        12.03         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         6.48         8.09        11.31        25.28        23.90 
TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        8.94        11.11         4.18        12.99        28.64        42.84 
TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 
       78.44         5.95        10.78         1.02        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       16.21        15.39        14.70 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            22.55              1.02 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            72.16             98.76 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           47.355            12.200 
[1] "22.6 - 72.2 (47.4)" "1.0 - 98.8 (12.2)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                57 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9        TCGA-D3-A2JD 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE        TCGA-D3-A3CF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV        TCGA-DA-A1HW 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB        TCGA-DA-A3F3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20F 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29R 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X        TCGA-EE-A2A0 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6        TCGA-ER-A19F 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-FR-A3YN        TCGA-FS-A4F9        TCGA-FW-A3R5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A267        TCGA-GN-A268 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A26D 
"9Q GAIN WILD-TYPE" 
D17V2, continuous
D17V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    2
  9Q GAIN WILD-TYPE   33   75
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               2                33
  MALE                 2                75
                   vv
clus                M0 M1 M1B M1C
  9Q GAIN MUTATED    4  0   0   0
  9Q GAIN WILD-TYPE 94  1   2   1
D17V4, multiclass
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0                4                94
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  9Q GAIN MUTATED    3  0   0   0  0   1   0   0  0  0
  9Q GAIN WILD-TYPE 58  1   3  10  1   2   8   1 13  2
D17V5, multiclass
D17V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9Q GAIN MUTATED             0       1        0        0        2         0
  9Q GAIN WILD-TYPE           1      14        7       11       11         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  9Q GAIN MUTATED           0         0         0          0          1
  9Q GAIN WILD-TYPE         5         2         4          3          9
                   vv
clus                STAGE IIIC STAGE IV
  9Q GAIN MUTATED            0        0
  9Q GAIN WILD-TYPE         18        3
D17V7, multiclass

Clustering(18) Variable = 11p gain mutation analysis
D18V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    2  2
  11P GAIN WILD-TYPE 25 30
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 55 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 30 
$`11P GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A3F3 TCGA-EE-A29T TCGA-ER-A19N 
       13.32         7.00         6.48        42.84 

$`11P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-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-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       22.36        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       12.20         4.27         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
        4.41         1.08         9.47        12.03         8.84         9.99 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F 
        8.09        11.31        25.28        23.90         8.94        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A 
        4.18        12.99        28.64        78.44         5.95        72.16 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       10.78         1.02        31.33        84.72        16.21        15.39 
TCGA-GN-A26D 
       14.70 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              6.48               1.02 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             42.84              98.76 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             10.16              12.99 
[1] "6.5 - 42.8 (10.2)" "1.0 - 98.8 (13.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D18V2, continuous
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    6
  11P GAIN WILD-TYPE   33   71
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                 33
  MALE                  6                 71
                    vv
clus                 M0 M1 M1B M1C
  11P GAIN MUTATED    7  0   0   0
  11P GAIN WILD-TYPE 91  1   2   1
D18V4, multiclass
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                 7                 91
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  11P GAIN MUTATED    3  0   1   1  0   0   1   0  0  1
  11P GAIN WILD-TYPE 58  1   2   9  1   3   7   1 13  1
D18V5, multiclass
D18V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11P GAIN MUTATED             0       1        0        0        1         1
  11P GAIN WILD-TYPE           1      14        7       11       12         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11P GAIN MUTATED           0         0         1          1          1
  11P GAIN WILD-TYPE         5         2         3          2          9
                    vv
clus                 STAGE IIIC STAGE IV
  11P GAIN MUTATED            0        0
  11P GAIN WILD-TYPE         18        3
D18V7, multiclass

Clustering(19) Variable = 11q gain mutation analysis
D19V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    1  2
  11Q GAIN WILD-TYPE 26 30
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 56 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 30 
$`11Q GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A3F3 TCGA-ER-A19N 
       13.32         7.00        42.84 

$`11Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-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-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       22.36        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       12.20         4.27         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
        4.41         1.08         9.47        12.03         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-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A1A1 TCGA-FR-A3YN 
       11.11         4.18        12.99        28.64        78.44         5.95 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       72.16        10.78         1.02        31.33        84.72        16.21 
TCGA-GN-A268 TCGA-GN-A26D 
       15.39        14.70 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              7.00               1.02 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             42.84              98.76 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            13.320             12.595 
[1] "7.0 - 42.8 (13.3)" "1.0 - 98.8 (12.6)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    4
  11Q GAIN WILD-TYPE   34   73
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                1                 34
  MALE                  4                 73
                    vv
clus                 M0 M1 M1B M1C
  11Q GAIN MUTATED    4  0   0   0
  11Q GAIN WILD-TYPE 94  1   2   1
D19V4, multiclass
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                 4                 94
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  11Q GAIN MUTATED    2  0   0   1  0   0   1   0  0  0
  11Q GAIN WILD-TYPE 59  1   3   9  1   3   7   1 13  2
D19V5, multiclass
D19V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11Q GAIN MUTATED             0       0        0        0        1         1
  11Q GAIN WILD-TYPE           1      15        7       11       12         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11Q GAIN MUTATED           0         0         1          0          1
  11Q GAIN WILD-TYPE         5         2         3          3          9
                    vv
clus                 STAGE IIIC STAGE IV
  11Q GAIN MUTATED            0        0
  11Q GAIN WILD-TYPE         18        3
D19V7, multiclass

Clustering(20) Variable = 12p gain mutation analysis
D20V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    2  6
  12P GAIN WILD-TYPE 25 26
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 8                 51 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 6                 26 
$`12P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-DA-A3F5 TCGA-EE-A2A6 TCGA-ER-A19J 
       16.47        22.55        13.32        17.56         8.94         4.18 
TCGA-ER-A19L TCGA-ER-A19M 
       12.99        28.64 

$`12P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        10.26         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       11.41         6.35        15.25        24.00         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 
       48.79        35.80        51.12        13.68        22.36         7.00 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        5.13        37.97        11.15        38.63         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
        9.47        12.03         8.84         9.99         6.48         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 
       11.31        25.28        23.90        11.11        42.84        78.44 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 
        5.95        72.16        10.78         1.02        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       16.21        15.39        14.70 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              4.18               1.02 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             28.64              98.76 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            14.895             12.030 
[1] "4.2 - 28.6 (14.9)" "1.0 - 98.8 (12.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "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-FR-A3YN 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "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-FR-A3YN 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "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-FR-A3YN 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2    8
  12P GAIN WILD-TYPE   33   69
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                2                 33
  MALE                  8                 69
                    vv
clus                 M0 M1 M1B M1C
  12P GAIN MUTATED    8  1   0   0
  12P GAIN WILD-TYPE 90  0   2   1
D20V4, multiclass
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                 8                 90
  M1                 1                  0
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  12P GAIN MUTATED    3  0   1   1  0   1   0   0  3  0
  12P GAIN WILD-TYPE 58  1   2   9  1   2   8   1 10  2
D20V5, multiclass
D20V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12P GAIN MUTATED             0       1        1        1        0         0
  12P GAIN WILD-TYPE           1      14        6       10       13         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12P GAIN MUTATED           0         0         1          1          1
  12P GAIN WILD-TYPE         5         2         3          2          9
                    vv
clus                 STAGE IIIC STAGE IV
  12P GAIN MUTATED            2        1
  12P GAIN WILD-TYPE         16        2
D20V7, multiclass

Clustering(21) Variable = 12q gain mutation analysis
D21V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    1  2
  12Q GAIN WILD-TYPE 26 30
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 56 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 30 
$`12Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-DA-A3F5 TCGA-ER-A19L 
       22.55        17.56        12.99 

$`12Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        32.55        98.76        28.08        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       22.36         7.00        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       12.20         4.27         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
        4.41         1.08         9.47        12.03         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-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN 
       11.11         4.18        28.64        42.84        78.44         5.95 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       72.16        10.78         1.02        31.33        84.72        16.21 
TCGA-GN-A268 TCGA-GN-A26D 
       15.39        14.70 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             12.99               1.02 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             22.55              98.76 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            17.560             12.115 
[1] "13.0 - 22.6 (17.6)" "1.0 - 98.8 (12.1)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0    4
  12Q GAIN WILD-TYPE   35   73
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                0                 35
  MALE                  4                 73
                    vv
clus                 M0 M1 M1B M1C
  12Q GAIN MUTATED    3  0   0   0
  12Q GAIN WILD-TYPE 95  1   2   1
D21V4, multiclass
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                 3                 95
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  12Q GAIN MUTATED    0  0   1   0  0   1   0   0  1  0
  12Q GAIN WILD-TYPE 61  1   2  10  1   2   8   1 12  2
D21V5, multiclass
D21V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12Q GAIN MUTATED             0       0        0        0        0         0
  12Q GAIN WILD-TYPE           1      15        7       11       13         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12Q GAIN MUTATED           0         0         0          1          1
  12Q GAIN WILD-TYPE         5         2         4          2          9
                    vv
clus                 STAGE IIIC STAGE IV
  12Q GAIN MUTATED            1        0
  12Q GAIN WILD-TYPE         17        3
D21V7, multiclass

Clustering(22) Variable = 13q gain mutation analysis
D22V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    3  7
  13Q GAIN WILD-TYPE 24 25
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                10                 49 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 7                 25 
$`13Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3CE TCGA-DA-A3F3 TCGA-EE-A29P TCGA-EE-A29R TCGA-ER-A19L 
       16.47        13.32         7.00        12.03         8.84        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       28.64        42.84        16.21        15.39 

$`13Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       32.55        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 
       21.14        11.41         6.35        15.25        24.00         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB 
        2.86        48.79        35.80        51.12        13.68        22.36 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        4.27         5.13        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        1.08         9.47         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A1A1 
       25.28        23.90         8.94        11.11         4.18        78.44 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 
        5.95        72.16        10.78         1.02        31.33        84.72 
TCGA-GN-A26D 
       14.70 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              7.00               1.02 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             42.84              98.76 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            14.355             11.570 
[1] "7.0 - 42.8 (14.4)" "1.0 - 98.8 (11.6)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D22V2, continuous
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      7    8
  13Q GAIN WILD-TYPE   28   69
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                7                 28
  MALE                  8                 69
                    vv
clus                 M0 M1 M1B M1C
  13Q GAIN MUTATED   12  0   0   0
  13Q GAIN WILD-TYPE 86  1   2   1
D22V4, multiclass
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                12                 86
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  13Q GAIN MUTATED    5  0   2   3  0   0   1   0  1  0
  13Q GAIN WILD-TYPE 56  1   1   7  1   3   7   1 12  2
D22V5, multiclass
D22V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  13Q GAIN MUTATED             0       1        0        2        0         0
  13Q GAIN WILD-TYPE           1      14        7        9       13         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  13Q GAIN MUTATED           1         1         1          2          1
  13Q GAIN WILD-TYPE         4         1         3          1          9
                    vv
clus                 STAGE IIIC STAGE IV
  13Q GAIN MUTATED            3        0
  13Q GAIN WILD-TYPE         15        3
D22V7, multiclass

Clustering(23) Variable = 14q gain mutation analysis
D23V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED    1  5
  14Q GAIN WILD-TYPE 26 27
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 6                 53 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 5                 27 
$`14Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-DA-A1I2 TCGA-EE-A29L TCGA-ER-A19L TCGA-ER-A19M TCGA-GN-A26D 
       22.55        13.68         1.08        12.99        28.64        14.70 

$`14Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        32.55        98.76        28.08        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1IB 
        4.01         2.86        48.79        35.80        51.12        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        7.00        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       12.20         4.27         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        4.41         9.47        12.03         8.84         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F 
        8.09        11.31        25.28        23.90         8.94        11.11 
TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 
        4.18        42.84        78.44         5.95        72.16        10.78 
TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.02        31.33        84.72        16.21        15.39 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.08               1.02 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             28.64              98.76 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             14.19              12.03 
[1] "1.1 - 28.6 (14.2)" "1.0 - 98.8 (12.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
[1] "hr=" "1.7"
D23V2, continuous
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    7
  14Q GAIN WILD-TYPE   33   70
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                2                 33
  MALE                  7                 70
                    vv
clus                 M0 M1 M1B M1C
  14Q GAIN MUTATED    7  0   0   0
  14Q GAIN WILD-TYPE 91  1   2   1
D23V4, multiclass
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                 7                 91
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  14Q GAIN MUTATED    5  0   0   0  0   1   1   0  1  0
  14Q GAIN WILD-TYPE 56  1   3  10  1   2   7   1 12  2
D23V5, multiclass
D23V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  14Q GAIN MUTATED             0       1        1        1        1         0
  14Q GAIN WILD-TYPE           1      14        6       10       12         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  14Q GAIN MUTATED           0         1         0          0          1
  14Q GAIN WILD-TYPE         5         1         4          3          9
                    vv
clus                 STAGE IIIC STAGE IV
  14Q GAIN MUTATED            2        0
  14Q GAIN WILD-TYPE         16        3
D23V7, multiclass

Clustering(24) Variable = 15q gain mutation analysis
D24V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    3  9
  15Q GAIN WILD-TYPE 24 23
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                12                 47 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 9                 23 
$`15Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A3CE TCGA-DA-A1HW TCGA-DA-A3F5 
       32.55        22.55        21.14        13.32        35.80        17.56 
TCGA-EE-A183 TCGA-EE-A29D TCGA-EE-A2A1 TCGA-ER-A19M TCGA-FR-A44A TCGA-GN-A264 
       12.20        11.15        25.28        28.64        72.16        31.33 

$`15Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JD 
       16.47        98.76        28.08        10.26         8.38        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-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X 
       51.12        13.68        22.36         7.00        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E 
        6.31         1.12         4.27         5.13        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
        4.41         1.08         9.47        12.03         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F 
        6.48         8.09        11.31        23.90         8.94        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FS-A4F9 
        4.18        12.99        42.84        78.44         5.95        10.78 
TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
        1.02        84.72        16.21        15.39        14.70 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             11.15               1.02 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             72.16              98.76 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            23.915             11.310 
[1] "11.2 - 72.2 (23.9)" "1.0 - 98.8 (11.3)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D24V2, continuous
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4   12
  15Q GAIN WILD-TYPE   31   65
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                4                 31
  MALE                 12                 65
                    vv
clus                 M0 M1 M1B M1C
  15Q GAIN MUTATED   15  0   0   0
  15Q GAIN WILD-TYPE 83  1   2   1
D24V4, multiclass
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                15                 83
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  15Q GAIN MUTATED    9  0   0   3  0   1   0   0  2  0
  15Q GAIN WILD-TYPE 52  1   3   7  1   2   8   1 11  2
D24V5, multiclass
D24V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  15Q GAIN MUTATED             1       3        1        2        1         1
  15Q GAIN WILD-TYPE           0      12        6        9       12         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  15Q GAIN MUTATED           0         0         1          0          2
  15Q GAIN WILD-TYPE         5         2         3          3          8
                    vv
clus                 STAGE IIIC STAGE IV
  15Q GAIN MUTATED            3        0
  15Q GAIN WILD-TYPE         15        3
D24V7, multiclass

Clustering(25) Variable = 16p gain mutation analysis
D25V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    1  2
  16P GAIN WILD-TYPE 26 30
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 56 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                 30 
$`16P GAIN MUTATED`
TCGA-D3-A3CE TCGA-EE-A29R TCGA-ER-A19M 
       13.32         8.84        28.64 

$`16P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        32.55        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF 
        8.38        21.14        11.41         6.35        15.25        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       22.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
        1.12        12.20         4.27         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S 
       38.63         4.41         1.08         9.47        12.03         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        6.48         8.09        11.31        25.28        23.90         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN 
       11.11         4.18        12.99        42.84        78.44         5.95 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       72.16        10.78         1.02        31.33        84.72        16.21 
TCGA-GN-A268 TCGA-GN-A26D 
       15.39        14.70 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              8.84               1.02 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             28.64              98.76 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            13.320             12.595 
[1] "8.8 - 28.6 (13.3)" "1.0 - 98.8 (12.6)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "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-FR-A3YN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "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-FR-A3YN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "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-FR-A3YN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3    3
  16P GAIN WILD-TYPE   32   74
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                3                 32
  MALE                  3                 74
                    vv
clus                 M0 M1 M1B M1C
  16P GAIN MUTATED    6  0   0   0
  16P GAIN WILD-TYPE 92  1   2   1
D25V4, multiclass
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                 6                 92
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  16P GAIN MUTATED    3  0   1   2  0   0   0   0  0  0
  16P GAIN WILD-TYPE 58  1   2   8  1   3   8   1 13  2
D25V5, multiclass
D25V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16P GAIN MUTATED             0       1        1        1        0         0
  16P GAIN WILD-TYPE           1      14        6       10       13         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16P GAIN MUTATED           0         0         1          1          0
  16P GAIN WILD-TYPE         5         2         3          2         10
                    vv
clus                 STAGE IIIC STAGE IV
  16P GAIN MUTATED            1        0
  16P GAIN WILD-TYPE         17        3
D25V7, multiclass

Clustering(26) Variable = 16q gain mutation analysis
D26V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    1  2
  16Q GAIN WILD-TYPE 26 30
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 56 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 30 
$`16Q GAIN MUTATED`
TCGA-D3-A3CE TCGA-EE-A29R TCGA-ER-A19M 
       13.32         8.84        28.64 

$`16Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        32.55        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF 
        8.38        21.14        11.41         6.35        15.25        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       22.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
        1.12        12.20         4.27         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S 
       38.63         4.41         1.08         9.47        12.03         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        6.48         8.09        11.31        25.28        23.90         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN 
       11.11         4.18        12.99        42.84        78.44         5.95 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       72.16        10.78         1.02        31.33        84.72        16.21 
TCGA-GN-A268 TCGA-GN-A26D 
       15.39        14.70 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              8.84               1.02 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             28.64              98.76 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            13.320             12.595 
[1] "8.8 - 28.6 (13.3)" "1.0 - 98.8 (12.6)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "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-FR-A3YN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "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-FR-A3YN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "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-FR-A3YN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2    4
  16Q GAIN WILD-TYPE   33   73
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                2                 33
  MALE                  4                 73
                    vv
clus                 M0 M1 M1B M1C
  16Q GAIN MUTATED    6  0   0   0
  16Q GAIN WILD-TYPE 92  1   2   1
D26V4, multiclass
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                 6                 92
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  16Q GAIN MUTATED    2  0   1   3  0   0   0   0  0  0
  16Q GAIN WILD-TYPE 59  1   2   7  1   3   8   1 13  2
D26V5, multiclass
D26V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16Q GAIN MUTATED             0       1        0        1        0         0
  16Q GAIN WILD-TYPE           1      14        7       10       13         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16Q GAIN MUTATED           0         0         1          1          1
  16Q GAIN WILD-TYPE         5         2         3          2          9
                    vv
clus                 STAGE IIIC STAGE IV
  16Q GAIN MUTATED            1        0
  16Q GAIN WILD-TYPE         17        3
D26V7, multiclass

Clustering(27) Variable = 17p gain mutation analysis
D27V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    4  3
  17P GAIN WILD-TYPE 23 29
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 7                 52 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 29 
$`17P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3CE TCGA-EE-A20F TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A2A6 
       16.47        13.32         5.13         9.47        12.03         8.94 
TCGA-GN-A26D 
       14.70 

$`17P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       32.55        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 
       21.14        11.41         6.35        15.25        24.00         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB 
        2.86        48.79        35.80        51.12        13.68        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        7.00        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       12.20         4.27        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        1.08         8.84         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       25.28        23.90        11.11         4.18        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 
       42.84        78.44         5.95        72.16        10.78         1.02 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       31.33        84.72        16.21        15.39 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              5.13               1.02 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             16.47              98.76 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            12.030             13.335 
[1] "5.1 - 16.5 (12.0)" "1.0 - 98.8 (13.3)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "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-FR-A3YN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "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-FR-A3YN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "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-FR-A3YN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
[1] "hr=" "1.2"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4    4
  17P GAIN WILD-TYPE   31   73
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                4                 31
  MALE                  4                 73
                    vv
clus                 M0 M1 M1B M1C
  17P GAIN MUTATED    7  0   0   0
  17P GAIN WILD-TYPE 91  1   2   1
D27V4, multiclass
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                 7                 91
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  17P GAIN MUTATED    6  0   0   1  0   0   0   0  1  0
  17P GAIN WILD-TYPE 55  1   3   9  1   3   8   1 12  2
D27V5, multiclass
D27V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17P GAIN MUTATED             0       0        1        0        1         1
  17P GAIN WILD-TYPE           1      15        6       11       12         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17P GAIN MUTATED           0         2         1          0          0
  17P GAIN WILD-TYPE         5         0         3          3         10
                    vv
clus                 STAGE IIIC STAGE IV
  17P GAIN MUTATED            1        0
  17P GAIN WILD-TYPE         17        3
D27V7, multiclass

Clustering(28) Variable = 17q gain mutation analysis
D28V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    5  6
  17Q GAIN WILD-TYPE 22 26
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                11                 48 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 6                 26 
$`17Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3CE TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29N 
       16.47        13.32         1.12         4.27         5.13         9.47 
TCGA-EE-A29P TCGA-EE-A2A6 TCGA-FR-A3YN TCGA-GN-A268 TCGA-GN-A26D 
       12.03         8.94         5.95        15.39        14.70 

$`17Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       32.55        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 
       21.14        11.41         6.35        15.25        24.00         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB 
        2.86        48.79        35.80        51.12        13.68        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 
        7.00        17.56        14.83        11.57         6.31        12.20 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29R 
       37.97        11.15        38.63         4.41         1.08         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         6.48         8.09        11.31        25.28        23.90 
TCGA-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-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       72.16        10.78         1.02        31.33        84.72        16.21 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              1.12               1.02 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             16.47              98.76 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             9.470             14.255 
[1] "1.1 - 16.5 (9.5)"  "1.0 - 98.8 (14.3)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "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-FR-A3YN 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "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-FR-A3YN 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "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-FR-A3YN 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
[1] "hr=" "2.1"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      7    8
  17Q GAIN WILD-TYPE   28   69
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                7                 28
  MALE                  8                 69
                    vv
clus                 M0 M1 M1B M1C
  17Q GAIN MUTATED   13  0   0   0
  17Q GAIN WILD-TYPE 85  1   2   1
D28V4, multiclass
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0                13                 85
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  17Q GAIN MUTATED   10  0   0   1  0   1   0   0  2  0
  17Q GAIN WILD-TYPE 51  1   3   9  1   2   8   1 11  2
D28V5, multiclass
D28V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17Q GAIN MUTATED             0       0        1        1        3         1
  17Q GAIN WILD-TYPE           1      15        6       10       10         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17Q GAIN MUTATED           1         2         1          0          0
  17Q GAIN WILD-TYPE         4         0         3          3         10
                    vv
clus                 STAGE IIIC STAGE IV
  17Q GAIN MUTATED            2        0
  17Q GAIN WILD-TYPE         16        3
D28V7, multiclass

Clustering(29) Variable = 18p gain mutation analysis
D29V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    3  6
  18P GAIN WILD-TYPE 24 26
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 9                 50 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                 26 
$`18P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29L 
       32.55        22.55        13.32         1.12        38.63         1.08 
TCGA-EE-A29P TCGA-GN-A267 TCGA-GN-A26D 
       12.03        16.21        14.70 

$`18P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       16.47        98.76        28.08        10.26         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       11.41         6.35        15.25        24.00         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 
       48.79        35.80        51.12        13.68        22.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 
       17.56        14.83        11.57         6.31        12.20         4.27 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29R 
        5.13        37.97        11.15         4.41         9.47         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         6.48         8.09        11.31        25.28        23.90 
TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        8.94        11.11         4.18        12.99        28.64        42.84 
TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 
       78.44         5.95        72.16        10.78         1.02        31.33 
TCGA-GN-A265 TCGA-GN-A268 
       84.72        15.39 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              1.08               1.02 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             38.63              98.76 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            14.700             11.885 
[1] "1.1 - 38.6 (14.7)" "1.0 - 98.8 (11.9)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
[1] "hr=" "1.2"
D29V2, continuous
D29V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6    8
  18P GAIN WILD-TYPE   29   69
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                6                 29
  MALE                  8                 69
                    vv
clus                 M0 M1 M1B M1C
  18P GAIN MUTATED   12  0   0   0
  18P GAIN WILD-TYPE 86  1   2   1
D29V4, multiclass
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                12                 86
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  18P GAIN MUTATED    7  0   2   2  0   1   0   0  1  0
  18P GAIN WILD-TYPE 54  1   1   8  1   2   8   1 12  2
D29V5, multiclass
D29V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18P GAIN MUTATED             1       3        0        0        1         0
  18P GAIN WILD-TYPE           0      12        7       11       12         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18P GAIN MUTATED           0         2         1          2          2
  18P GAIN WILD-TYPE         5         0         3          1          8
                    vv
clus                 STAGE IIIC STAGE IV
  18P GAIN MUTATED            1        0
  18P GAIN WILD-TYPE         17        3
D29V7, multiclass

Clustering(30) Variable = 18q gain mutation analysis
D30V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    1  3
  18Q GAIN WILD-TYPE 26 29
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 55 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 29 
$`18Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-EE-A29L TCGA-GN-A267 TCGA-GN-A26D 
       32.55         1.08        16.21        14.70 

$`18Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       22.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
        1.12        12.20         4.27         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
       38.63         4.41         9.47        12.03         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-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-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 
        5.95        72.16        10.78         1.02        31.33        84.72 
TCGA-GN-A268 
       15.39 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              1.08               1.02 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             32.55              98.76 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            15.455             12.200 
[1] "1.1 - 32.5 (15.5)" "1.0 - 98.8 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
[1] "hr=" "1.3"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    5
  18Q GAIN WILD-TYPE   34   72
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 34
  MALE                  5                 72
                    vv
clus                 M0 M1 M1B M1C
  18Q GAIN MUTATED    4  0   0   0
  18Q GAIN WILD-TYPE 94  1   2   1
D30V4, multiclass
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                 4                 94
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  18Q GAIN MUTATED    3  0   1   0  0   0   0   0  1  0
  18Q GAIN WILD-TYPE 58  1   2  10  1   3   8   1 12  2
D30V5, multiclass
D30V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18Q GAIN MUTATED             1       1        0        0        0         0
  18Q GAIN WILD-TYPE           0      14        7       11       13         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18Q GAIN MUTATED           0         1         0          1          0
  18Q GAIN WILD-TYPE         5         1         4          2         10
                    vv
clus                 STAGE IIIC STAGE IV
  18Q GAIN MUTATED            1        0
  18Q GAIN WILD-TYPE         17        3
D30V7, multiclass

Clustering(31) Variable = 19p gain mutation analysis
D31V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    1  3
  19P GAIN WILD-TYPE 26 29
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                 55 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                 29 
$`19P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3CE TCGA-EE-A29L TCGA-EE-A29R 
       32.55        13.32         1.08         8.84 

$`19P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 
       21.14        11.41         6.35        15.25        24.00         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB 
        2.86        48.79        35.80        51.12        13.68        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        7.00        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       12.20         4.27         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
        4.41         9.47        12.03         9.99         6.48         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J 
       11.31        25.28        23.90         8.94        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A 
       12.99        28.64        42.84        78.44         5.95        72.16 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       10.78         1.02        31.33        84.72        16.21        15.39 
TCGA-GN-A26D 
       14.70 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              1.08               1.02 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             32.55              98.76 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             11.08              12.99 
[1] "1.1 - 32.5 (11.1)" "1.0 - 98.8 (13.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      4    4
  19P GAIN WILD-TYPE   31   73
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                4                 31
  MALE                  4                 73
                    vv
clus                 M0 M1 M1B M1C
  19P GAIN MUTATED    8  0   0   0
  19P GAIN WILD-TYPE 90  1   2   1
D31V4, multiclass
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                 8                 90
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  19P GAIN MUTATED    5  0   0   2  0   0   0   0  1  0
  19P GAIN WILD-TYPE 56  1   3   8  1   3   8   1 12  2
D31V5, multiclass
D31V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19P GAIN MUTATED             1       2        0        1        0         1
  19P GAIN WILD-TYPE           0      13        7       10       13         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19P GAIN MUTATED           0         0         1          0          0
  19P GAIN WILD-TYPE         5         2         3          3         10
                    vv
clus                 STAGE IIIC STAGE IV
  19P GAIN MUTATED            2        0
  19P GAIN WILD-TYPE         16        3
D31V7, multiclass

Clustering(32) Variable = 19q gain mutation analysis
D32V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    2  4
  19Q GAIN WILD-TYPE 25 28
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                 53 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                 28 
$`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 

$`19Q GAIN WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       98.76        28.08        22.55        10.26         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       11.41         6.35        15.25        24.00         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 
       48.79        35.80        51.12        13.68        22.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        4.27         5.13        37.97        11.15        38.63         4.41 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.47        12.03         9.99         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       23.90         8.94        11.11         4.18        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 
       42.84        78.44         5.95        72.16        10.78         1.02 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       31.33        84.72        16.21        15.39        14.70 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              1.08               1.02 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             32.55              98.76 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             11.08              12.99 
[1] "1.1 - 32.5 (11.1)" "1.0 - 98.8 (13.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D32V2, continuous
D32V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      5    4
  19Q GAIN WILD-TYPE   30   73
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                5                 30
  MALE                  4                 73
                    vv
clus                 M0 M1 M1B M1C
  19Q GAIN MUTATED    9  0   0   0
  19Q GAIN WILD-TYPE 89  1   2   1
D32V4, multiclass
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                 9                 89
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  19Q GAIN MUTATED    4  0   0   2  0   0   0   0  2  1
  19Q GAIN WILD-TYPE 57  1   3   8  1   3   8   1 11  1
D32V5, multiclass
D32V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19Q GAIN MUTATED             1       1        0        1        0         1
  19Q GAIN WILD-TYPE           0      14        7       10       13         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19Q GAIN MUTATED           0         0         1          0          0
  19Q GAIN WILD-TYPE         5         2         3          3         10
                    vv
clus                 STAGE IIIC STAGE IV
  19Q GAIN MUTATED            3        0
  19Q GAIN WILD-TYPE         15        3
D32V7, multiclass

Clustering(33) Variable = 20p gain mutation analysis
D33V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED    6  9
  20P GAIN WILD-TYPE 21 23
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                15                 44 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 9                 23 
$`20P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-DA-A1I2 TCGA-DA-A3F5 
       16.47        32.55        22.55        13.32        13.68        17.56 
TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        8.84        25.28         8.94         4.18        12.99        28.64 
TCGA-FR-A3YN TCGA-GN-A264 TCGA-GN-A26D 
        5.95        31.33        14.70 

$`20P GAIN WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       98.76        28.08        10.26         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-A1HY TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X 
       35.80        51.12        22.36         7.00        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C 
        6.31         1.12        12.20         4.27         5.13        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       11.15        38.63         4.41         1.08         9.47        12.03 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-ER-A19F 
        9.99         6.48         8.09        11.31        23.90        11.11 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A265 
       42.84        78.44        72.16        10.78         1.02        84.72 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              4.18               1.02 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             32.55              98.76 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             14.70              11.49 
[1] "4.2 - 32.5 (14.7)" "1.0 - 98.8 (11.5)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "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-FR-A3YN 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "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-FR-A3YN 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "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-FR-A3YN 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
[1] "hr=" "1.1"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     10   21
  20P GAIN WILD-TYPE   25   56
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               10                 25
  MALE                 21                 56
                    vv
clus                 M0 M1 M1B M1C
  20P GAIN MUTATED   26  1   0   0
  20P GAIN WILD-TYPE 72  0   2   1
D33V4, multiclass
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0                26                 72
  M1                 1                  0
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  20P GAIN MUTATED   17  0   1   3  0   1   2   0  3  1
  20P GAIN WILD-TYPE 44  1   2   7  1   2   6   1 10  1
D33V5, multiclass
D33V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  20P GAIN MUTATED             1       5        4        3        2         1
  20P GAIN WILD-TYPE           0      10        3        8       11         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  20P GAIN MUTATED           0         1         1          1          1
  20P GAIN WILD-TYPE         5         1         3          2          9
                    vv
clus                 STAGE IIIC STAGE IV
  20P GAIN MUTATED            6        1
  20P GAIN WILD-TYPE         12        2
D33V7, multiclass

Clustering(34) Variable = 20q gain mutation analysis
D34V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   10 10
  20Q GAIN WILD-TYPE 17 22
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                20                 39 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                 22 
$`20Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-DA-A1HV TCGA-DA-A1I2 
       16.47        32.55        22.55        13.32        48.79        13.68 
TCGA-DA-A3F5 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A1 
       17.56        38.63         1.08        12.03         8.84        25.28 
TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-FR-A3YN TCGA-FR-A44A 
        8.94         4.18        12.99        28.64         5.95        72.16 
TCGA-GN-A264 TCGA-GN-A26D 
       31.33        14.70 

$`20Q GAIN WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       98.76        28.08        10.26         8.38        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW 
        6.35        15.25        24.00         4.01         2.86        35.80 
TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       51.12        22.36         7.00        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
        1.12        12.20         4.27         5.13        37.97        11.15 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        4.41         9.47         9.99         6.48         8.09        11.31 
TCGA-EE-A2A2 TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FS-A4F9 TCGA-FW-A3R5 
       23.90        11.11        42.84        78.44        10.78         1.02 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       84.72        16.21        15.39 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              1.08               1.02 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             72.16              98.76 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            15.585             11.310 
[1] "1.1 - 72.2 (15.6)" "1.0 - 98.8 (11.3)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "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-FR-A3YN 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "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-FR-A3YN 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "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-FR-A3YN 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
[1] "hr=" "1.5"
D34V2, continuous
D34V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     13   26
  20Q GAIN WILD-TYPE   22   51
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               13                 22
  MALE                 26                 51
                    vv
clus                 M0 M1 M1B M1C
  20Q GAIN MUTATED   32  1   1   0
  20Q GAIN WILD-TYPE 66  0   1   1
D34V4, multiclass
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0                32                 66
  M1                 1                  0
  M1B                1                  1
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  20Q GAIN MUTATED   20  0   1   4  0   1   3   0  5  1
  20Q GAIN WILD-TYPE 41  1   2   6  1   2   5   1  8  1
D34V5, multiclass
D34V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  20Q GAIN MUTATED             1       5        4        3        4         1
  20Q GAIN WILD-TYPE           0      10        3        8        9         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  20Q GAIN MUTATED           0         2         1          1          3
  20Q GAIN WILD-TYPE         5         0         3          2          7
                    vv
clus                 STAGE IIIC STAGE IV
  20Q GAIN MUTATED            7        1
  20Q GAIN WILD-TYPE         11        2
D34V7, multiclass

Clustering(35) Variable = 21q gain mutation analysis
D35V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    4  3
  21Q GAIN WILD-TYPE 23 29
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                 52 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 29 
$`21Q GAIN MUTATED`
TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-ER-A19L TCGA-FR-A3YN 
        1.08         8.84        11.31        25.28        12.99         5.95 
TCGA-GN-A26D 
       14.70 

$`21Q 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-A3CE 
        8.38        21.14        11.41         6.35        15.25        13.32 
TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       24.00         4.01         2.86        48.79        35.80        51.12 
TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
       13.68        22.36         7.00        17.56        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C 
        6.31         1.12        12.20         4.27         5.13        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S 
       11.15        38.63         4.41         9.47        12.03         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J 
        6.48         8.09        23.90         8.94        11.11         4.18 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 
       28.64        42.84        78.44        72.16        10.78         1.02 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       31.33        84.72        16.21        15.39 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              1.08               1.02 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             25.28              98.76 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             11.31              13.50 
[1] "1.1 - 25.3 (11.3)" "1.0 - 98.8 (13.5)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "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-FR-A3YN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "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-FR-A3YN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "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-FR-A3YN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
[1] "hr=" "1.3"
D35V2, continuous
D35V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5    6
  21Q GAIN WILD-TYPE   30   71
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                5                 30
  MALE                  6                 71
                    vv
clus                 M0 M1 M1B M1C
  21Q GAIN MUTATED    9  0   0   0
  21Q GAIN WILD-TYPE 89  1   2   1
D35V4, multiclass
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                 9                 89
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  21Q GAIN MUTATED    7  0   0   1  0   1   0   0  1  0
  21Q GAIN WILD-TYPE 54  1   3   9  1   2   8   1 12  2
D35V5, multiclass
D35V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  21Q GAIN MUTATED             0       1        0        2        1         2
  21Q GAIN WILD-TYPE           1      14        7        9       12         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  21Q GAIN MUTATED           0         1         0          1          0
  21Q GAIN WILD-TYPE         5         1         4          2         10
                    vv
clus                 STAGE IIIC STAGE IV
  21Q GAIN MUTATED            2        0
  21Q GAIN WILD-TYPE         16        3
D35V7, multiclass

Clustering(36) Variable = 22q gain mutation analysis
D36V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    8  7
  22Q GAIN WILD-TYPE 19 25
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                15                 44 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 7                 25 
$`22Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-DA-A1HV TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EE-A29L 
       16.47        22.55        48.79        22.36        17.56         1.08 
TCGA-EE-A29N TCGA-EE-A29R TCGA-ER-A19M TCGA-FR-A3YN TCGA-FR-A44A TCGA-GN-A264 
        9.47         8.84        28.64         5.95        72.16        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26D 
       84.72        16.21        14.70 

$`22Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        10.26         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 
       11.41         6.35        15.25        13.32        24.00         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A3F3 TCGA-DA-A3F8 
        2.86        35.80        51.12        13.68         7.00        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
       11.57         6.31         1.12        12.20         4.27         5.13 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29S 
       37.97        11.15        38.63         4.41        12.03         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        6.48         8.09        11.31        25.28        23.90         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FS-A4F9 
       11.11         4.18        12.99        42.84        78.44        10.78 
TCGA-FW-A3R5 TCGA-GN-A268 
        1.02        15.39 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.08               1.02 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             84.72              98.76 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             17.56              11.49 
[1] "1.1 - 84.7 (17.6)" "1.0 - 98.8 (11.5)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
[1] "hr=" "1.7"
D36V2, continuous
D36V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      8   16
  22Q GAIN WILD-TYPE   27   61
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                8                 27
  MALE                 16                 61
                    vv
clus                 M0 M1 M1B M1C
  22Q GAIN MUTATED   20  0   1   0
  22Q GAIN WILD-TYPE 78  1   1   1
D36V4, multiclass
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                20                 78
  M1                 0                  1
  M1B                1                  1
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  22Q GAIN MUTATED   11  0   2   1  0   2   2   0  4  0
  22Q GAIN WILD-TYPE 50  1   1   9  1   1   6   1  9  2
D36V5, multiclass
D36V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  22Q GAIN MUTATED             0       2        1        2        3         1
  22Q GAIN WILD-TYPE           1      13        6        9       10         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  22Q GAIN MUTATED           0         1         0          3          2
  22Q GAIN WILD-TYPE         5         1         4          0          8
                    vv
clus                 STAGE IIIC STAGE IV
  22Q GAIN MUTATED            5        0
  22Q GAIN WILD-TYPE         13        3
D36V7, multiclass

Clustering(37) Variable = 1p loss mutation analysis
D37V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    2  2
  1P LOSS WILD-TYPE 25 30
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4                55 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                30 
$`1P LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-EE-A29R TCGA-ER-A19L TCGA-GN-A26D 
       22.55         8.84        12.99        14.70 

$`1P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        32.55        98.76        28.08        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       22.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
        1.12        12.20         4.27         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S 
       38.63         4.41         1.08         9.47        12.03         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        6.48         8.09        11.31        25.28        23.90         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN 
       11.11         4.18        28.64        42.84        78.44         5.95 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       72.16        10.78         1.02        31.33        84.72        16.21 
TCGA-GN-A268 
       15.39 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             8.84              1.02 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            22.55             98.76 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           13.845            12.200 
[1] "8.8 - 22.6 (13.8)" "1.0 - 98.8 (12.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
[1] "hr=" "1"  
D37V2, continuous
D37V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4    4
  1P LOSS WILD-TYPE   31   73
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               4                31
  MALE                 4                73
                   vv
clus                M0 M1 M1B M1C
  1P LOSS MUTATED    5  0   0   0
  1P LOSS WILD-TYPE 93  1   2   1
D37V4, multiclass
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0                5                93
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  1P LOSS MUTATED    3  0   0   1  0   1   1   0  0  0
  1P LOSS WILD-TYPE 58  1   3   9  1   2   7   1 13  2
D37V5, multiclass
D37V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1P LOSS MUTATED             0       0        0        0        2         0
  1P LOSS WILD-TYPE           1      15        7       11       11         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1P LOSS MUTATED           0         1         1          0          1
  1P LOSS WILD-TYPE         5         1         3          3          9
                   vv
clus                STAGE IIIC STAGE IV
  1P LOSS MUTATED            1        0
  1P LOSS WILD-TYPE         17        3
D37V7, multiclass

Clustering(38) Variable = 2p loss mutation analysis
D38V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    3  4
  2P LOSS WILD-TYPE 24 28
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7                52 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4                28 
$`2P LOSS MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z3 TCGA-DA-A1I2 TCGA-EE-A20F TCGA-GN-A264 
       15.25        24.00         2.86        13.68         5.13        31.33 
TCGA-GN-A26D 
       14.70 

$`2P LOSS 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-A3CE TCGA-D9-A3Z1 
        8.38        21.14        11.41         6.35        13.32         4.01 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 
       48.79        35.80        51.12        22.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       37.97        11.15        38.63         4.41         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
       12.03         8.84         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       25.28        23.90         8.94        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 
       28.64        42.84        78.44         5.95        72.16        10.78 
TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.02        84.72        16.21        15.39 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.86              1.02 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            31.33             98.76 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           14.700            12.115 
[1] "2.9 - 31.3 (14.7)" "1.0 - 98.8 (12.1)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
[1] "hr=" "1.1"
D38V2, continuous
D38V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4    8
  2P LOSS WILD-TYPE   31   69
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               4                31
  MALE                 8                69
                   vv
clus                M0 M1 M1B M1C
  2P LOSS MUTATED    9  0   0   0
  2P LOSS WILD-TYPE 89  1   2   1
D38V4, multiclass
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0                9                89
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  2P LOSS MUTATED    7  0   0   1  0   0   1   0  1  0
  2P LOSS WILD-TYPE 54  1   3   9  1   3   7   1 12  2
D38V5, multiclass
D38V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2P LOSS MUTATED             0       0        0        2        3         0
  2P LOSS WILD-TYPE           1      15        7        9       10         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  2P LOSS MUTATED           1         1         0          0          1
  2P LOSS WILD-TYPE         4         1         4          3          9
                   vv
clus                STAGE IIIC STAGE IV
  2P LOSS MUTATED            2        0
  2P LOSS WILD-TYPE         16        3
D38V7, multiclass

Clustering(39) Variable = 2q loss mutation analysis
D39V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    2  3
  2Q LOSS WILD-TYPE 25 29
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5                54 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                29 
$`2Q LOSS MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-EE-A20F TCGA-EE-A29D TCGA-GN-A26D 
       15.25        24.00         5.13        11.15        14.70 

$`2Q LOSS 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-A3CE TCGA-D9-A3Z1 
        8.38        21.14        11.41         6.35        13.32         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB 
        2.86        48.79        35.80        51.12        13.68        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        7.00        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
       12.20         4.27        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-A29X 
        9.47        12.03         8.84         9.99         6.48         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J 
       11.31        25.28        23.90         8.94        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A 
       12.99        28.64        42.84        78.44         5.95        72.16 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       10.78         1.02        31.33        84.72        16.21        15.39 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             5.13              1.02 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            24.00             98.76 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           14.700            12.595 
[1] "5.1 - 24.0 (14.7)" "1.0 - 98.8 (12.6)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
[1] "hr=" "1.4"
D39V2, continuous
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    6
  2Q LOSS WILD-TYPE   30   71
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               5                30
  MALE                 6                71
                   vv
clus                M0 M1 M1B M1C
  2Q LOSS MUTATED    8  0   1   0
  2Q LOSS WILD-TYPE 90  1   1   1
D39V4, multiclass
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0                8                90
  M1                0                 1
  M1B               1                 1
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  2Q LOSS MUTATED    7  0   0   1  0   0   0   0  2  0
  2Q LOSS WILD-TYPE 54  1   3   9  1   3   8   1 11  2
D39V5, multiclass
D39V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2Q LOSS MUTATED             0       0        0        2        3         0
  2Q LOSS WILD-TYPE           1      15        7        9       10         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  2Q LOSS MUTATED           1         1         0          0          0
  2Q LOSS WILD-TYPE         4         1         4          3         10
                   vv
clus                STAGE IIIC STAGE IV
  2Q LOSS MUTATED            2        0
  2Q LOSS WILD-TYPE         16        3
D39V7, multiclass

Clustering(40) Variable = 3p loss mutation analysis
D40V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    0  4
  3P LOSS WILD-TYPE 27 28
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                55 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                28 
$`3P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3C6 TCGA-DA-A1HW TCGA-DA-A1I2 
       32.55        15.25        35.80        13.68 

$`3P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 
       21.14        11.41         6.35        13.32        24.00         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 
        2.86        48.79        51.12        22.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        5.13        37.97        11.15        38.63         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
        9.47        12.03         8.84         9.99         6.48         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J 
       11.31        25.28        23.90         8.94        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A 
       12.99        28.64        42.84        78.44         5.95        72.16 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       10.78         1.02        31.33        84.72        16.21        15.39 
TCGA-GN-A26D 
       14.70 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            13.68              1.02 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            35.80             98.76 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            23.90             12.03 
[1] "13.7 - 35.8 (23.9)" "1.0 - 98.8 (12.0)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2    3
  3P LOSS WILD-TYPE   33   74
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               2                33
  MALE                 3                74
                   vv
clus                M0 M1 M1B M1C
  3P LOSS MUTATED    5  0   0   0
  3P LOSS WILD-TYPE 93  1   2   1
D40V4, multiclass
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0                5                93
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  3P LOSS MUTATED    3  0   0   1  0   0   1   0  0  0
  3P LOSS WILD-TYPE 58  1   3   9  1   3   7   1 13  2
D40V5, multiclass
D40V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3P LOSS MUTATED             1       1        0        1        0         0
  3P LOSS WILD-TYPE           0      14        7       10       13         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  3P LOSS MUTATED           0         0         0          0          1
  3P LOSS WILD-TYPE         5         2         4          3          9
                   vv
clus                STAGE IIIC STAGE IV
  3P LOSS MUTATED            1        0
  3P LOSS WILD-TYPE         17        3
D40V7, multiclass

Clustering(41) Variable = 3q loss mutation analysis
D41V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    1  6
  3Q LOSS WILD-TYPE 26 26
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                7                52 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6                26 
$`3Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3C6 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EE-A29H TCGA-GN-A264 
       32.55        15.25        35.80        13.68         4.41        31.33 
TCGA-GN-A268 
       15.39 

$`3Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 
       21.14        11.41         6.35        13.32        24.00         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 
        2.86        48.79        51.12        22.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N 
        5.13        37.97        11.15        38.63         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
       12.03         8.84         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       25.28        23.90         8.94        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 
       28.64        42.84        78.44         5.95        72.16        10.78 
TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26D 
        1.02        84.72        16.21        14.70 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             4.41              1.02 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            35.80             98.76 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            15.39             11.80 
[1] "4.4 - 35.8 (15.4)" "1.0 - 98.8 (11.8)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D41V2, continuous
D41V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      4    4
  3Q LOSS WILD-TYPE   31   73
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               4                31
  MALE                 4                73
                   vv
clus                M0 M1 M1B M1C
  3Q LOSS MUTATED    7  0   0   0
  3Q LOSS WILD-TYPE 91  1   2   1
D41V4, multiclass
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0                7                91
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  3Q LOSS MUTATED    5  0   0   1  0   0   1   0  0  0
  3Q LOSS WILD-TYPE 56  1   3   9  1   3   7   1 13  2
D41V5, multiclass
D41V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3Q LOSS MUTATED             1       0        2        1        0         0
  3Q LOSS WILD-TYPE           0      15        5       10       13         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  3Q LOSS MUTATED           1         0         0          0          1
  3Q LOSS WILD-TYPE         4         2         4          3          9
                   vv
clus                STAGE IIIC STAGE IV
  3Q LOSS MUTATED            1        0
  3Q LOSS WILD-TYPE         17        3
D41V7, multiclass

Clustering(42) Variable = 4p loss mutation analysis
D42V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    2  3
  4P LOSS WILD-TYPE 25 29
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5                54 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                29 
$`4P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-EE-A29C 
       16.47        10.26         2.86        35.80        37.97 

$`4P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        22.55         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 
       11.41         6.35        15.25        13.32        24.00         4.01 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 
       48.79        51.12        13.68        22.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
        5.13        11.15        38.63         4.41         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
       12.03         8.84         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       25.28        23.90         8.94        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 
       28.64        42.84        78.44         5.95        72.16        10.78 
TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
        1.02        31.33        84.72        16.21        15.39        14.70 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             2.86              1.02 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            37.97             98.76 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           16.470            12.595 
[1] "2.9 - 38.0 (16.5)" "1.0 - 98.8 (12.6)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       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-FR-A3YN        TCGA-FR-A44A 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       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-FR-A3YN        TCGA-FR-A44A 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       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-FR-A3YN        TCGA-FR-A44A 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      4    5
  4P LOSS WILD-TYPE   31   72
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               4                31
  MALE                 5                72
                   vv
clus                M0 M1 M1B M1C
  4P LOSS MUTATED    8  0   1   0
  4P LOSS WILD-TYPE 90  1   1   1
D42V4, multiclass
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0                8                90
  M1                0                 1
  M1B               1                 1
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  4P LOSS MUTATED    4  0   0   2  0   1   0   0  2  0
  4P LOSS WILD-TYPE 57  1   3   8  1   2   8   1 11  2
D42V5, multiclass
D42V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4P LOSS MUTATED             0       1        0        1        1         0
  4P LOSS WILD-TYPE           1      14        7       10       12         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4P LOSS MUTATED           1         0         0          1          2
  4P LOSS WILD-TYPE         4         2         4          2          8
                   vv
clus                STAGE IIIC STAGE IV
  4P LOSS MUTATED            1        0
  4P LOSS WILD-TYPE         17        3
D42V7, multiclass

Clustering(43) Variable = 4q loss mutation analysis
D43V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    2  4
  4Q LOSS WILD-TYPE 25 28
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                6                53 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                28 
$`4Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-EE-A181 TCGA-EE-A29C 
       16.47        28.08         2.86        35.80         1.12        37.97 

$`4Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        22.55        10.26         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 
       11.41         6.35        15.25        13.32        24.00         4.01 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 
       48.79        51.12        13.68        22.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
       14.83        11.57         6.31        12.20         4.27         5.13 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       11.15        38.63         4.41         1.08         9.47        12.03 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       23.90         8.94        11.11         4.18        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 
       42.84        78.44         5.95        72.16        10.78         1.02 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       31.33        84.72        16.21        15.39        14.70 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             1.12              1.02 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            37.97             98.76 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           22.275            12.200 
[1] "1.1 - 38.0 (22.3)" "1.0 - 98.8 (12.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       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-FR-A3YN        TCGA-FR-A44A 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       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-FR-A3YN        TCGA-FR-A44A 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       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-FR-A3YN        TCGA-FR-A44A 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D43V2, continuous
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      5    5
  4Q LOSS WILD-TYPE   30   72
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               5                30
  MALE                 5                72
                   vv
clus                M0 M1 M1B M1C
  4Q LOSS MUTATED    8  0   2   0
  4Q LOSS WILD-TYPE 90  1   0   1
D43V4, multiclass
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0                8                90
  M1                0                 1
  M1B               2                 0
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  4Q LOSS MUTATED    4  0   0   2  0   1   0   0  3  0
  4Q LOSS WILD-TYPE 57  1   3   8  1   2   8   1 10  2
D43V5, multiclass
D43V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4Q LOSS MUTATED             0       1        0        1        2         0
  4Q LOSS WILD-TYPE           1      14        7       10       11         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4Q LOSS MUTATED           0         0         0          1          2
  4Q LOSS WILD-TYPE         5         2         4          2          8
                   vv
clus                STAGE IIIC STAGE IV
  4Q LOSS MUTATED            1        1
  4Q LOSS WILD-TYPE         17        2
D43V7, multiclass

Clustering(44) Variable = 5p loss mutation analysis
D44V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    4  4
  5P LOSS WILD-TYPE 23 28
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                8                51 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                28 
$`5P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29E 
       16.47        48.79        11.57         4.27        37.97        38.63 
TCGA-EE-A2A2 TCGA-GN-A268 
       23.90        15.39 

$`5P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       32.55        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB 
        4.01         2.86        35.80        51.12        13.68        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
        7.00        17.56        14.83         6.31         1.12        12.20 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
        5.13        11.15         4.41         1.08         9.47        12.03 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        8.94        11.11         4.18        12.99        28.64        42.84 
TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 
       78.44         5.95        72.16        10.78         1.02        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26D 
       84.72        16.21        14.70 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             4.27              1.02 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            48.79             98.76 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           20.185            12.030 
[1] "4.3 - 48.8 (20.2)" "1.0 - 98.8 (12.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "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-FR-A3YN        TCGA-FR-A44A 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "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-FR-A3YN        TCGA-FR-A44A 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "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-FR-A3YN        TCGA-FR-A44A 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D44V2, continuous
D44V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      7    7
  5P LOSS WILD-TYPE   28   70
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               7                28
  MALE                 7                70
                   vv
clus                M0 M1 M1B M1C
  5P LOSS MUTATED   13  0   0   0
  5P LOSS WILD-TYPE 85  1   2   1
D44V4, multiclass
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               13                85
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  5P LOSS MUTATED    6  0   0   2  0   1   2   0  2  0
  5P LOSS WILD-TYPE 55  1   3   8  1   2   6   1 11  2
D44V5, multiclass
D44V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5P LOSS MUTATED             0       2        2        1        0         0
  5P LOSS WILD-TYPE           1      13        5       10       13         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5P LOSS MUTATED           1         0         0          1          3
  5P LOSS WILD-TYPE         4         2         4          2          7
                   vv
clus                STAGE IIIC STAGE IV
  5P LOSS MUTATED            3        0
  5P LOSS WILD-TYPE         15        3
D44V7, multiclass

Clustering(45) Variable = 5q loss mutation analysis
D45V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    5  8
  5Q LOSS WILD-TYPE 22 24
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               13                46 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                8                24 
$`5Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1HV 
       28.08         6.35        15.25        24.00         4.01        48.79 
TCGA-DA-A1HW TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2A2 
       35.80        11.57         4.27        37.97        38.63        23.90 
TCGA-GN-A268 
       15.39 

$`5Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        32.55        98.76        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D9-A3Z3 TCGA-DA-A1HY TCGA-DA-A1I2 
       21.14        11.41        13.32         2.86        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17Z TCGA-EE-A181 
       22.36         7.00        17.56        14.83         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       12.20         5.13        11.15         4.41         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
       12.03         8.84         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       25.28         8.94        11.11         4.18        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 
       42.84        78.44         5.95        72.16        10.78         1.02 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26D 
       31.33        84.72        16.21        14.70 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             4.01              1.02 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            48.79             98.76 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            23.90             11.72 
[1] "4.0 - 48.8 (23.9)" "1.0 - 98.8 (11.7)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "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-FR-A3YN        TCGA-FR-A44A 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "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-FR-A3YN        TCGA-FR-A44A 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "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-FR-A3YN        TCGA-FR-A44A 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D45V2, continuous
D45V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     10   14
  5Q LOSS WILD-TYPE   25   63
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              10                25
  MALE                14                63
                   vv
clus                M0 M1 M1B M1C
  5Q LOSS MUTATED   21  0   1   0
  5Q LOSS WILD-TYPE 77  1   1   1
D45V4, multiclass
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               21                77
  M1                0                 1
  M1B               1                 1
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  5Q LOSS MUTATED   10  0   0   3  0   1   3   0  4  1
  5Q LOSS WILD-TYPE 51  1   3   7  1   2   5   1  9  1
D45V5, multiclass
D45V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5Q LOSS MUTATED             0       3        2        2        1         1
  5Q LOSS WILD-TYPE           1      12        5        9       12         4
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5Q LOSS MUTATED           1         0         0          1          4
  5Q LOSS WILD-TYPE         4         2         4          2          6
                   vv
clus                STAGE IIIC STAGE IV
  5Q LOSS MUTATED            5        1
  5Q LOSS WILD-TYPE         13        2
D45V7, multiclass

Clustering(46) Variable = 6p loss mutation analysis
D46V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED    2  6
  6P LOSS WILD-TYPE 25 26
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8                51 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                26 
$`6P LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A3CE TCGA-EE-A29D TCGA-EE-A29X TCGA-EE-A2A0 
       22.55        10.26        13.32        11.15         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 
       25.28        23.90 

$`6P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 
       16.47        32.55        98.76        28.08         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       11.41         6.35        15.25        24.00         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 
       48.79        35.80        51.12        13.68        22.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        4.27         5.13        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-A2A6 
        9.47        12.03         8.84         9.99         6.48         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 
        5.95        72.16        10.78         1.02        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       16.21        15.39        14.70 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             8.09              1.02 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            25.28             98.76 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           12.315            12.990 
[1] "8.1 - 25.3 (12.3)" "1.0 - 98.8 (13.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "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-FR-A3YN        TCGA-FR-A44A 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "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-FR-A3YN        TCGA-FR-A44A 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "6P LOSS MUTATED"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "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-FR-A3YN        TCGA-FR-A44A 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D46V2, continuous
D46V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3    6
  6P LOSS WILD-TYPE   32   71
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               3                32
  MALE                 6                71
                   vv
clus                M0 M1 M1B M1C
  6P LOSS MUTATED    9  0   0   0
  6P LOSS WILD-TYPE 89  1   2   1
D46V4, multiclass
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0                9                89
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  6P LOSS MUTATED    5  0   0   3  0   1   0   0  0  0
  6P LOSS WILD-TYPE 56  1   3   7  1   2   8   1 13  2
D46V5, multiclass
D46V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6P LOSS MUTATED             0       0        0        2        1         1
  6P LOSS WILD-TYPE           1      15        7        9       12         4
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6P LOSS MUTATED           1         0         1          0          2
  6P LOSS WILD-TYPE         4         2         3          3          8
                   vv
clus                STAGE IIIC STAGE IV
  6P LOSS MUTATED            1        0
  6P LOSS WILD-TYPE         17        3
D46V7, multiclass

Clustering(47) Variable = 6q loss mutation analysis
D47V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   12 14
  6Q LOSS WILD-TYPE 15 18
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               26                33 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               14                18 
$`6Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A3C6 TCGA-D3-A3CE 
       16.47        32.55        22.55        10.26        15.25        13.32 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A3F5 TCGA-EE-A185 TCGA-EE-A29C 
        2.86        48.79        51.12        17.56         4.27        37.97 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       11.15         4.41         9.99         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N TCGA-FW-A3R5 
       23.90         8.94        11.11         4.18        42.84         1.02 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

$`6Q LOSS WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       98.76        28.08         8.38        21.14        11.41         6.35 
TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 
       24.00         4.01        35.80        13.68        22.36         7.00 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F 
       14.83        11.57         6.31         1.12        12.20         5.13 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T 
       38.63         1.08         9.47        12.03         8.84         6.48 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 
       12.99        28.64        78.44         5.95        72.16        10.78 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26D 
       31.33        84.72        14.70 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             1.02              1.08 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            51.12             98.76 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           14.285            12.200 
[1] "1.0 - 51.1 (14.3)" "1.1 - 98.8 (12.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "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 MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-FR-A3YN        TCGA-FR-A44A 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "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 MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-FR-A3YN        TCGA-FR-A44A 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "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 MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-FR-A3YN        TCGA-FR-A44A 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D47V2, continuous
D47V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     14   26
  6Q LOSS WILD-TYPE   21   51
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              14                21
  MALE                26                51
                   vv
clus                M0 M1 M1B M1C
  6Q LOSS MUTATED   34  1   1   1
  6Q LOSS WILD-TYPE 64  0   1   0
D47V4, multiclass
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0               34                64
  M1                1                 0
  M1B               1                 1
  M1C               1                 0
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  6Q LOSS MUTATED   17  0   2   5  1   2   2   1  6  1
  6Q LOSS WILD-TYPE 44  1   1   5  0   1   6   0  7  1
D47V5, multiclass
D47V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6Q LOSS MUTATED             1       1        3        5        2         2
  6Q LOSS WILD-TYPE           0      14        4        6       11         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6Q LOSS MUTATED           2         0         2          1          6
  6Q LOSS WILD-TYPE         3         2         2          2          4
                   vv
clus                STAGE IIIC STAGE IV
  6Q LOSS MUTATED            6        2
  6Q LOSS WILD-TYPE         12        1
D47V7, multiclass

Clustering(48) Variable = 8p loss mutation analysis
D48V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    2  4
  8P LOSS WILD-TYPE 25 28
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                6                53 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                28 
$`8P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3C6 TCGA-EE-A183 TCGA-EE-A29C TCGA-EE-A29H TCGA-GN-A264 
       16.47        15.25        12.20        37.97         4.41        31.33 

$`8P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       32.55        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 
       21.14        11.41         6.35        13.32        24.00         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB 
        2.86        48.79        35.80        51.12        13.68        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        7.00        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N 
        4.27         5.13        11.15        38.63         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
       12.03         8.84         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       25.28        23.90         8.94        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 
       28.64        42.84        78.44         5.95        72.16        10.78 
TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
        1.02        84.72        16.21        15.39        14.70 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             4.41              1.02 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            37.97             98.76 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            15.86             12.03 
[1] "4.4 - 38.0 (15.9)" "1.0 - 98.8 (12.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "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-FR-A3YN        TCGA-FR-A44A 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "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-FR-A3YN        TCGA-FR-A44A 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "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-FR-A3YN        TCGA-FR-A44A 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D48V2, continuous
D48V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5    9
  8P LOSS WILD-TYPE   30   68
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               5                30
  MALE                 9                68
                   vv
clus                M0 M1 M1B M1C
  8P LOSS MUTATED   10  0   1   0
  8P LOSS WILD-TYPE 88  1   1   1
D48V4, multiclass
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0               10                88
  M1                0                 1
  M1B               1                 1
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  8P LOSS MUTATED    8  0   0   0  0   1   0   0  2  0
  8P LOSS WILD-TYPE 53  1   3  10  1   2   8   1 11  2
D48V5, multiclass
D48V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8P LOSS MUTATED             0       4        1        2        1         0
  8P LOSS WILD-TYPE           1      11        6        9       12         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8P LOSS MUTATED           0         0         0          0          0
  8P LOSS WILD-TYPE         5         2         4          3         10
                   vv
clus                STAGE IIIC STAGE IV
  8P LOSS MUTATED            1        0
  8P LOSS WILD-TYPE         17        3
D48V7, multiclass

Clustering(49) Variable = 8q loss mutation analysis
D49V1, survival
                   sevent
clus2                0  1
  8Q LOSS WILD-TYPE 27 32
8Q LOSS WILD-TYPE 
               59 
[1] 32
$`8Q LOSS 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-A3CE 
        8.38        21.14        11.41         6.35        15.25        13.32 
TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       24.00         4.01         2.86        48.79        35.80        51.12 
TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
       13.68        22.36         7.00        17.56        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C 
        6.31         1.12        12.20         4.27         5.13        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       11.15        38.63         4.41         1.08         9.47        12.03 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       23.90         8.94        11.11         4.18        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 
       42.84        78.44         5.95        72.16        10.78         1.02 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       31.33        84.72        16.21        15.39        14.70 

8Q LOSS WILD-TYPE 
             1.02 
8Q LOSS WILD-TYPE 
            98.76 
8Q LOSS WILD-TYPE 
            12.99 
[1] "1.0 - 98.8 (13.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D49V2, continuous
D49V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    1
  8Q LOSS WILD-TYPE   33   76
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               2                33
  MALE                 1                76
                   vv
clus                M0 M1 M1B M1C
  8Q LOSS MUTATED    3  0   0   0
  8Q LOSS WILD-TYPE 95  1   2   1
D49V4, multiclass
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0                3                95
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  8Q LOSS MUTATED    3  0   0   0  0   0   0   0  0  0
  8Q LOSS WILD-TYPE 58  1   3  10  1   3   8   1 13  2
D49V5, multiclass
D49V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8Q LOSS MUTATED             0       2        0        0        1         0
  8Q LOSS WILD-TYPE           1      13        7       11       12         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8Q LOSS MUTATED           0         0         0          0          0
  8Q LOSS WILD-TYPE         5         2         4          3         10
                   vv
clus                STAGE IIIC STAGE IV
  8Q LOSS MUTATED            0        0
  8Q LOSS WILD-TYPE         18        3
D49V7, multiclass

Clustering(50) Variable = 9p loss mutation analysis
D50V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   12 21
  9P LOSS WILD-TYPE 15 11
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               33                26 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               21                11 
$`9P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JK TCGA-D3-A3C6 
       16.47        32.55        28.08        10.26         6.35        15.25 
TCGA-D3-A3CF TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
       24.00         2.86        48.79        35.80        51.12        13.68 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
       11.57         1.12         4.27         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29X 
       38.63         1.08         9.47        12.03         9.99         8.09 
TCGA-EE-A2A0 TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-FR-A3YN TCGA-FS-A4F9 
       11.31        11.11        12.99        28.64         5.95        10.78 
TCGA-FW-A3R5 TCGA-GN-A268 TCGA-GN-A26D 
        1.02        15.39        14.70 

$`9P LOSS WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE 
       98.76        22.55         8.38        21.14        11.41        13.32 
TCGA-D9-A3Z1 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17Z 
        4.01        22.36         7.00        17.56        14.83         6.31 
TCGA-EE-A183 TCGA-EE-A29H TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 
       12.20         4.41         8.84         6.48        25.28        23.90 
TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A44A TCGA-GN-A264 
        8.94         4.18        42.84        78.44        72.16        31.33 
TCGA-GN-A265 TCGA-GN-A267 
       84.72        16.21 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             1.02              4.01 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            51.12             98.76 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            11.57             15.52 
[1] "1.0 - 51.1 (11.6)" "4.0 - 98.8 (15.5)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       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-FR-A3YN        TCGA-FR-A44A 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       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-FR-A3YN        TCGA-FR-A44A 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       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-FR-A3YN        TCGA-FR-A44A 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
[1] "hr=" "1.8"
D50V2, continuous
D50V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     17   40
  9P LOSS WILD-TYPE   18   37
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              17                18
  MALE                40                37
                   vv
clus                M0 M1 M1B M1C
  9P LOSS MUTATED   49  0   2   1
  9P LOSS WILD-TYPE 49  1   0   0
D50V4, multiclass
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0               49                49
  M1                0                 1
  M1B               2                 0
  M1C               1                 0
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  9P LOSS MUTATED   32  0   2   6  1   0   3   1  8  0
  9P LOSS WILD-TYPE 29  1   1   4  0   3   5   0  5  2
D50V5, multiclass
D50V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9P LOSS MUTATED             1       2        3        7        9         3
  9P LOSS WILD-TYPE           0      13        4        4        4         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  9P LOSS MUTATED           3         2         1          1          6
  9P LOSS WILD-TYPE         2         0         3          2          4
                   vv
clus                STAGE IIIC STAGE IV
  9P LOSS MUTATED           10        2
  9P LOSS WILD-TYPE          8        1
D50V7, multiclass

Clustering(51) Variable = 9q loss mutation analysis
D51V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    7 15
  9Q LOSS WILD-TYPE 20 17
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               22                37 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               15                17 
$`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-A1I2 TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29N 
       13.68         1.12         5.13        11.15         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-ER-A19F 
       12.03         9.99         8.09        11.31        23.90        11.11 
TCGA-ER-A19M TCGA-FW-A3R5 TCGA-GN-A268 TCGA-GN-A26D 
       28.64         1.02        15.39        14.70 

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

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             1.02              2.86 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            48.79             98.76 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           12.855            12.990 
[1] "1.0 - 48.8 (12.9)" "2.9 - 98.8 (13.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       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-FR-A3YN        TCGA-FR-A44A 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       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-FR-A3YN        TCGA-FR-A44A 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       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-FR-A3YN        TCGA-FR-A44A 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
[1] "hr=" "1.7"
D51V2, continuous
D51V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     16   26
  9Q LOSS WILD-TYPE   19   51
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              16                19
  MALE                26                51
                   vv
clus                M0 M1 M1B M1C
  9Q LOSS MUTATED   35  0   2   1
  9Q LOSS WILD-TYPE 63  1   0   0
D51V4, multiclass
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0               35                63
  M1                0                 1
  M1B               2                 0
  M1C               1                 0
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  9Q LOSS MUTATED   24  0   2   3  1   1   3   1  4  0
  9Q LOSS WILD-TYPE 37  1   1   7  0   2   5   0  9  2
D51V5, multiclass
D51V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9Q LOSS MUTATED             1       1        2        5        7         2
  9Q LOSS WILD-TYPE           0      14        5        6        6         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  9Q LOSS MUTATED           2         2         2          2          4
  9Q LOSS WILD-TYPE         3         0         2          1          6
                   vv
clus                STAGE IIIC STAGE IV
  9Q LOSS MUTATED            4        2
  9Q LOSS WILD-TYPE         14        1
D51V7, multiclass

Clustering(52) Variable = 10p loss mutation analysis
D52V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    6 16
  10P LOSS WILD-TYPE 21 16
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                22                 37 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                16                 16 
$`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-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EE-A17Z TCGA-EE-A185 
       24.00         2.86        35.80        13.68         6.31         4.27 
TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29X TCGA-ER-A19L 
        5.13         4.41         1.08        12.03         8.09        12.99 
TCGA-FR-A3YN TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
        5.95        31.33        16.21        15.39 

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

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              1.08               1.02 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             98.76              84.72 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            13.155             12.200 
[1] "1.1 - 98.8 (13.2)" "1.0 - 84.7 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "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-FR-A3YN 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "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-FR-A3YN 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "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-FR-A3YN 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D52V2, continuous
D52V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     20   25
  10P LOSS WILD-TYPE   15   52
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               20                 15
  MALE                 25                 52
                    vv
clus                 M0 M1 M1B M1C
  10P LOSS MUTATED   40  0   1   1
  10P LOSS WILD-TYPE 58  1   1   0
D52V4, multiclass
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                40                 58
  M1                 0                  1
  M1B                1                  1
  M1C                1                  0
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  10P LOSS MUTATED   26  0   2   4  0   0   4   1  5  0
  10P LOSS WILD-TYPE 35  1   1   6  1   3   4   0  8  2
D52V5, multiclass
D52V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  10P LOSS MUTATED             1       5        5        4        6         1
  10P LOSS WILD-TYPE           0      10        2        7        7         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  10P LOSS MUTATED           3         1         2          2          2
  10P LOSS WILD-TYPE         2         1         2          1          8
                    vv
clus                 STAGE IIIC STAGE IV
  10P LOSS MUTATED            8        2
  10P LOSS WILD-TYPE         10        1
D52V7, multiclass

Clustering(53) Variable = 10q loss mutation analysis
D53V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    8 16
  10Q LOSS WILD-TYPE 19 16
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                24                 35 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                16                 16 
$`10Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JK 
       16.47        32.55        98.76        28.08        22.55         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A3F8 
       15.25        13.32         2.86        35.80        13.68        14.83 
TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P 
        6.31         4.27         5.13         4.41         1.08        12.03 
TCGA-EE-A29X TCGA-EE-A2A6 TCGA-ER-A19L TCGA-FR-A3YN TCGA-GN-A264 TCGA-GN-A267 
        8.09         8.94        12.99         5.95        31.33        16.21 

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

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              1.08               1.02 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             98.76              84.72 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            13.155             12.200 
[1] "1.1 - 98.8 (13.2)" "1.0 - 84.7 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"10Q LOSS WILD-TYPE"   "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-FR-A3YN 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"10Q LOSS WILD-TYPE"   "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-FR-A3YN 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"10Q LOSS WILD-TYPE"   "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-FR-A3YN 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D53V2, continuous
D53V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     19   30
  10Q LOSS WILD-TYPE   16   47
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               19                 16
  MALE                 30                 47
                    vv
clus                 M0 M1 M1B M1C
  10Q LOSS MUTATED   42  0   2   1
  10Q LOSS WILD-TYPE 56  1   0   0
D53V4, multiclass
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                42                 56
  M1                 0                  1
  M1B                2                  0
  M1C                1                  0
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  10Q LOSS MUTATED   28  0   2   4  0   1   4   1  5  0
  10Q LOSS WILD-TYPE 33  1   1   6  1   2   4   0  8  2
D53V5, multiclass
D53V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  10Q LOSS MUTATED             1       5        6        5        6         1
  10Q LOSS WILD-TYPE           0      10        1        6        7         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  10Q LOSS MUTATED           3         1         2          2          4
  10Q LOSS WILD-TYPE         2         1         2          1          6
                    vv
clus                 STAGE IIIC STAGE IV
  10Q LOSS MUTATED            6        2
  10Q LOSS WILD-TYPE         12        1
D53V7, multiclass

Clustering(54) Variable = 11p loss mutation analysis
D54V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    7 11
  11P LOSS WILD-TYPE 20 21
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                18                 41 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                11                 21 
$`11P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       16.47        32.55        22.55        10.26         2.86        48.79 
TCGA-DA-A1HW TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29X 
       35.80        37.97        11.15         1.08         8.84         8.09 
TCGA-EE-A2A2 TCGA-ER-A19L TCGA-FR-A3YN TCGA-FS-A4F9 TCGA-GN-A264 TCGA-GN-A267 
       23.90        12.99         5.95        10.78        31.33        16.21 

$`11P LOSS WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       98.76        28.08         8.38        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1HY TCGA-DA-A1I2 
       15.25        13.32        24.00         4.01        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       22.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29H 
        1.12        12.20         4.27         5.13        38.63         4.41 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.47        12.03         9.99         6.48        11.31        25.28 
TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
        8.94        11.11         4.18        28.64        42.84        78.44 
TCGA-FR-A44A TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D 
       72.16         1.02        84.72        15.39        14.70 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              1.08               1.02 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             48.79              98.76 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              14.6               12.2 
[1] "1.1 - 48.8 (14.6)" "1.0 - 98.8 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "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-FR-A3YN 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "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-FR-A3YN 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "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-FR-A3YN 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D54V2, continuous
D54V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      8   18
  11P LOSS WILD-TYPE   27   59
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                8                 27
  MALE                 18                 59
                    vv
clus                 M0 M1 M1B M1C
  11P LOSS MUTATED   21  0   0   1
  11P LOSS WILD-TYPE 77  1   2   0
D54V4, multiclass
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                21                 77
  M1                 0                  1
  M1B                0                  2
  M1C                1                  0
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  11P LOSS MUTATED    9  0   1   5  0   1   1   1  3  1
  11P LOSS WILD-TYPE 52  1   2   5  1   2   7   0 10  1
D54V5, multiclass
D54V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11P LOSS MUTATED             1       1        1        3        1         0
  11P LOSS WILD-TYPE           0      14        6        8       12         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11P LOSS MUTATED           2         0         0          1          5
  11P LOSS WILD-TYPE         3         2         4          2          5
                    vv
clus                 STAGE IIIC STAGE IV
  11P LOSS MUTATED            5        1
  11P LOSS WILD-TYPE         13        2
D54V7, multiclass

Clustering(55) Variable = 11q loss mutation analysis
D55V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    8 10
  11Q LOSS WILD-TYPE 19 22
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                18                 41 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                10                 22 
$`11Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D9-A3Z3 
       16.47        32.55        98.76        22.55        10.26         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29R 
       48.79        35.80        37.97        11.15         1.08         8.84 
TCGA-EE-A2A2 TCGA-ER-A19L TCGA-FR-A3YN TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26D 
       23.90        12.99         5.95        31.33        16.21        14.70 

$`11Q LOSS WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       28.08         8.38        21.14        11.41         6.35        15.25 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB 
       13.32        24.00         4.01        51.12        13.68        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        7.00        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N 
       12.20         4.27         5.13        38.63         4.41         9.47 
TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       12.03         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
        8.94        11.11         4.18        28.64        42.84        78.44 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A268 
       72.16        10.78         1.02        84.72        15.39 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              1.08               1.02 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             98.76              84.72 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             16.34              11.57 
[1] "1.1 - 98.8 (16.3)" "1.0 - 84.7 (11.6)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "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-FR-A3YN 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "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-FR-A3YN 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "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-FR-A3YN 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
[1] "hr=" "1.3"
D55V2, continuous
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     10   20
  11Q LOSS WILD-TYPE   25   57
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               10                 25
  MALE                 20                 57
                    vv
clus                 M0 M1 M1B M1C
  11Q LOSS MUTATED   24  0   0   1
  11Q LOSS WILD-TYPE 74  1   2   0
D55V4, multiclass
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                24                 74
  M1                 0                  1
  M1B                0                  2
  M1C                1                  0
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  11Q LOSS MUTATED   12  0   2   6  0   1   1   1  2  1
  11Q LOSS WILD-TYPE 49  1   1   4  1   2   7   0 11  1
D55V5, multiclass
D55V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11Q LOSS MUTATED             1       2        1        4        1         0
  11Q LOSS WILD-TYPE           0      13        6        7       12         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11Q LOSS MUTATED           2         1         0          2          5
  11Q LOSS WILD-TYPE         3         1         4          1          5
                    vv
clus                 STAGE IIIC STAGE IV
  11Q LOSS MUTATED            5        1
  11Q LOSS WILD-TYPE         13        2
D55V7, multiclass

Clustering(56) Variable = 12p loss mutation analysis
D56V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    2  1
  12P LOSS WILD-TYPE 25 31
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                 56 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 31 
$`12P LOSS MUTATED`
TCGA-D3-A2J6 TCGA-EE-A29S TCGA-EE-A2A2 
       10.26         9.99        23.90 

$`12P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J8 
       16.47        32.55        98.76        28.08        22.55         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       22.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
        1.12        12.20         4.27         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       38.63         4.41         1.08         9.47        12.03         8.84 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19F 
        6.48         8.09        11.31        25.28         8.94        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN 
        4.18        12.99        28.64        42.84        78.44         5.95 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       72.16        10.78         1.02        31.33        84.72        16.21 
TCGA-GN-A268 TCGA-GN-A26D 
       15.39        14.70 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              9.99               1.02 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             23.90              98.76 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            10.260             13.155 
[1] "10.0 - 23.9 (10.3)" "1.0 - 98.8 (13.2)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "12P LOSS MUTATED" "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-FR-A3YN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "12P LOSS MUTATED" "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-FR-A3YN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "12P LOSS MUTATED" "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-FR-A3YN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D56V2, continuous
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    3
  12P LOSS WILD-TYPE   33   74
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                2                 33
  MALE                  3                 74
                    vv
clus                 M0 M1 M1B M1C
  12P LOSS MUTATED    4  0   0   1
  12P LOSS WILD-TYPE 94  1   2   0
D56V4, multiclass
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                 4                 94
  M1                 0                  1
  M1B                0                  2
  M1C                1                  0
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  12P LOSS MUTATED    3  0   0   1  0   0   0   1  0  0
  12P LOSS WILD-TYPE 58  1   3   9  1   3   8   0 13  2
D56V5, multiclass
D56V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12P LOSS MUTATED             0       0        0        0        1         1
  12P LOSS WILD-TYPE           1      15        7       11       12         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12P LOSS MUTATED           1         0         0          0          1
  12P LOSS WILD-TYPE         4         2         4          3          9
                    vv
clus                 STAGE IIIC STAGE IV
  12P LOSS MUTATED            0        1
  12P LOSS WILD-TYPE         18        2
D56V7, multiclass

Clustering(57) Variable = 12q loss mutation analysis
D57V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    2  2
  12Q LOSS WILD-TYPE 25 30
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 55 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                 30 
$`12Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 
       16.47         9.99         8.09        23.90 

$`12Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       32.55        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       22.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
        1.12        12.20         4.27         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       38.63         4.41         1.08         9.47        12.03         8.84 
TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J 
        6.48        11.31        25.28         8.94        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A 
       12.99        28.64        42.84        78.44         5.95        72.16 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       10.78         1.02        31.33        84.72        16.21        15.39 
TCGA-GN-A26D 
       14.70 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              8.09               1.02 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             23.90              98.76 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             13.23              12.99 
[1] "8.1 - 23.9 (13.2)" "1.0 - 98.8 (13.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "12Q LOSS MUTATED" "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-FR-A3YN 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "12Q LOSS MUTATED" "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-FR-A3YN 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "12Q LOSS MUTATED" "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-FR-A3YN 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D57V2, continuous
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      5    3
  12Q LOSS WILD-TYPE   30   74
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                5                 30
  MALE                  3                 74
                    vv
clus                 M0 M1 M1B M1C
  12Q LOSS MUTATED    6  0   0   1
  12Q LOSS WILD-TYPE 92  1   2   0
D57V4, multiclass
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                 6                 92
  M1                 0                  1
  M1B                0                  2
  M1C                1                  0
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  12Q LOSS MUTATED    4  0   0   1  0   0   0   1  1  0
  12Q LOSS WILD-TYPE 57  1   3   9  1   3   8   0 12  2
D57V5, multiclass
D57V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12Q LOSS MUTATED             0       0        1        1        1         1
  12Q LOSS WILD-TYPE           1      15        6       10       12         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12Q LOSS MUTATED           0         0         0          0          1
  12Q LOSS WILD-TYPE         5         2         4          3          9
                    vv
clus                 STAGE IIIC STAGE IV
  12Q LOSS MUTATED            1        1
  12Q LOSS WILD-TYPE         17        2
D57V7, multiclass

Clustering(58) Variable = 13q loss mutation analysis
D58V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    6  5
  13Q LOSS WILD-TYPE 21 27
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                11                 48 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                 27 
$`13Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-EE-A181 TCGA-EE-A29C 
       28.08         2.86        48.79        13.68         1.12        37.97 
TCGA-EE-A29D TCGA-EE-A29N TCGA-EE-A29T TCGA-FR-A3YN TCGA-GN-A26D 
       11.15         9.47         6.48         5.95        14.70 

$`13Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        32.55        98.76        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.01        35.80        51.12        22.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
       14.83        11.57         6.31        12.20         4.27         5.13 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
       38.63         4.41         1.08        12.03         8.84         9.99 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F 
        8.09        11.31        25.28        23.90         8.94        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A44A 
        4.18        12.99        28.64        42.84        78.44        72.16 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       10.78         1.02        31.33        84.72        16.21        15.39 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              1.12               1.02 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             48.79              98.76 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            11.150             13.155 
[1] "1.1 - 48.8 (11.2)" "1.0 - 98.8 (13.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
[1] "hr=" "1.1"
D58V2, continuous
D58V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      5   12
  13Q LOSS WILD-TYPE   30   65
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                5                 30
  MALE                 12                 65
                    vv
clus                 M0 M1 M1B M1C
  13Q LOSS MUTATED   12  0   2   1
  13Q LOSS WILD-TYPE 86  1   0   0
D58V4, multiclass
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                12                 86
  M1                 0                  1
  M1B                2                  0
  M1C                1                  0
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  13Q LOSS MUTATED    8  0   0   2  0   0   2   1  2  1
  13Q LOSS WILD-TYPE 53  1   3   8  1   3   6   0 11  1
D58V5, multiclass
D58V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  13Q LOSS MUTATED             0       0        1        2        3         0
  13Q LOSS WILD-TYPE           1      15        6        9       10         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  13Q LOSS MUTATED           0         1         0          0          2
  13Q LOSS WILD-TYPE         5         1         4          3          8
                    vv
clus                 STAGE IIIC STAGE IV
  13Q LOSS MUTATED            2        2
  13Q LOSS WILD-TYPE         16        1
D58V7, multiclass

Clustering(59) Variable = 14q loss mutation analysis
D59V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED    6  8
  14Q LOSS WILD-TYPE 21 24
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                14                 45 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 8                 24 
$`14Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A3CE TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A3F5 
       16.47        10.26        13.32        48.79        51.12        17.56 
TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29X TCGA-EE-A2A6 TCGA-FS-A4F9 TCGA-GN-A264 
        1.12        37.97         8.09         8.94        10.78        31.33 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

$`14Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        22.55         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       11.41         6.35        15.25        24.00         4.01         2.86 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X 
       35.80        13.68        22.36         7.00        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E 
        6.31        12.20         4.27         5.13        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
        4.41         1.08         9.47        12.03         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19F TCGA-ER-A19J 
        6.48        11.31        25.28        23.90        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A 
       12.99        28.64        42.84        78.44         5.95        72.16 
TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A26D 
        1.02        84.72        14.70 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              1.12               1.02 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             51.12              98.76 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             15.80              12.03 
[1] "1.1 - 51.1 (15.8)" "1.0 - 98.8 (12.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "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-FR-A3YN 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "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-FR-A3YN 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "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-FR-A3YN 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D59V2, continuous
D59V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      8   17
  14Q LOSS WILD-TYPE   27   60
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                8                 27
  MALE                 17                 60
                    vv
clus                 M0 M1 M1B M1C
  14Q LOSS MUTATED   23  0   0   1
  14Q LOSS WILD-TYPE 75  1   2   0
D59V4, multiclass
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0                23                 75
  M1                 0                  1
  M1B                0                  2
  M1C                1                  0
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  14Q LOSS MUTATED   15  0   1   2  0   0   1   1  4  0
  14Q LOSS WILD-TYPE 46  1   2   8  1   3   7   0  9  2
D59V5, multiclass
D59V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  14Q LOSS MUTATED             0       3        1        2        7         0
  14Q LOSS WILD-TYPE           1      12        6        9        6         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  14Q LOSS MUTATED           2         0         1          1          1
  14Q LOSS WILD-TYPE         3         2         3          2          9
                    vv
clus                 STAGE IIIC STAGE IV
  14Q LOSS MUTATED            5        1
  14Q LOSS WILD-TYPE         13        2
D59V7, multiclass

Clustering(60) Variable = 15q loss mutation analysis
D60V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    1  3
  15Q LOSS WILD-TYPE 26 29
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                 55 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                 29 
$`15Q LOSS MUTATED`
TCGA-D3-A3C6 TCGA-EE-A29L TCGA-EE-A29P TCGA-GN-A267 
       15.25         1.08        12.03        16.21 

$`15Q LOSS 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-A3CE TCGA-D3-A3CF 
        8.38        21.14        11.41         6.35        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       22.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
        1.12        12.20         4.27         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       38.63         4.41         9.47         8.84         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F 
        8.09        11.31        25.28        23.90         8.94        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN 
        4.18        12.99        28.64        42.84        78.44         5.95 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
       72.16        10.78         1.02        31.33        84.72        15.39 
TCGA-GN-A26D 
       14.70 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              1.08               1.02 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             16.21              98.76 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             13.64              12.99 
[1] "1.1 - 16.2 (13.6)" "1.0 - 98.8 (13.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
[1] "hr=" "2"  
D60V2, continuous
D60V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3    4
  15Q LOSS WILD-TYPE   32   73
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                3                 32
  MALE                  4                 73
                    vv
clus                 M0 M1 M1B M1C
  15Q LOSS MUTATED    5  0   1   0
  15Q LOSS WILD-TYPE 93  1   1   1
D60V4, multiclass
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                 5                 93
  M1                 0                  1
  M1B                1                  1
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  15Q LOSS MUTATED    3  0   1   0  0   0   0   0  2  0
  15Q LOSS WILD-TYPE 58  1   2  10  1   3   8   1 11  2
D60V5, multiclass
D60V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  15Q LOSS MUTATED             0       0        0        1        1         0
  15Q LOSS WILD-TYPE           1      15        7       10       12         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  15Q LOSS MUTATED           0         1         0          1          0
  15Q LOSS WILD-TYPE         5         1         4          2         10
                    vv
clus                 STAGE IIIC STAGE IV
  15Q LOSS MUTATED            1        0
  15Q LOSS WILD-TYPE         17        3
D60V7, multiclass

Clustering(61) Variable = 16p loss mutation analysis
D61V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    0  6
  16P LOSS WILD-TYPE 27 26
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                 53 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                 26 
$`16P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EE-A17Z TCGA-EE-A29D TCGA-EE-A29X 
       32.55        35.80        13.68         6.31        11.15         8.09 

$`16P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F3 
        4.01         2.86        48.79        51.12        22.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       17.56        14.83        11.57         1.12        12.20         4.27 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
        5.13        37.97        38.63         4.41         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 
       12.03         8.84         9.99         6.48        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       23.90         8.94        11.11         4.18        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 
       42.84        78.44         5.95        72.16        10.78         1.02 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       31.33        84.72        16.21        15.39        14.70 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              6.31               1.02 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             35.80              98.76 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            12.415             12.990 
[1] "6.3 - 35.8 (12.4)" "1.0 - 98.8 (13.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D61V2, continuous
D61V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    5
  16P LOSS WILD-TYPE   32   72
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                 32
  MALE                  5                 72
                    vv
clus                 M0 M1 M1B M1C
  16P LOSS MUTATED    8  0   0   0
  16P LOSS WILD-TYPE 90  1   2   1
D61V4, multiclass
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                 8                 90
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  16P LOSS MUTATED    5  0   0   2  0   0   1   0  0  0
  16P LOSS WILD-TYPE 56  1   3   8  1   3   7   1 13  2
D61V5, multiclass
D61V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16P LOSS MUTATED             1       0        0        1        1         0
  16P LOSS WILD-TYPE           0      15        7       10       12         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16P LOSS MUTATED           2         0         0          0          1
  16P LOSS WILD-TYPE         3         2         4          3          9
                    vv
clus                 STAGE IIIC STAGE IV
  16P LOSS MUTATED            2        0
  16P LOSS WILD-TYPE         16        3
D61V7, multiclass

Clustering(62) Variable = 16q loss mutation analysis
D62V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    2  8
  16Q LOSS WILD-TYPE 25 24
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                 49 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 8                 24 
$`16Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A3F8 TCGA-EE-A17Z 
       32.55         2.86        35.80        13.68        14.83         6.31 
TCGA-EE-A185 TCGA-EE-A29D TCGA-EE-A29X TCGA-GN-A267 
        4.27        11.15         8.09        16.21 

$`16Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.01        48.79        51.12        22.36         7.00        17.56 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E 
       11.57         1.12        12.20         5.13        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
        4.41         1.08         9.47        12.03         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F 
        6.48        11.31        25.28        23.90         8.94        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN 
        4.18        12.99        28.64        42.84        78.44         5.95 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
       72.16        10.78         1.02        31.33        84.72        15.39 
TCGA-GN-A26D 
       14.70 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              2.86               1.02 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             35.80              98.76 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            12.415             12.990 
[1] "2.9 - 35.8 (12.4)" "1.0 - 98.8 (13.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26D 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D62V2, continuous
D62V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5   11
  16Q LOSS WILD-TYPE   30   66
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                5                 30
  MALE                 11                 66
                    vv
clus                 M0 M1 M1B M1C
  16Q LOSS MUTATED   14  0   1   0
  16Q LOSS WILD-TYPE 84  1   1   1
D62V4, multiclass
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0                14                 84
  M1                 0                  1
  M1B                1                  1
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  16Q LOSS MUTATED    7  0   1   3  0   0   2   0  2  0
  16Q LOSS WILD-TYPE 54  1   2   7  1   3   6   1 11  2
D62V5, multiclass
D62V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16Q LOSS MUTATED             1       0        0        1        3         0
  16Q LOSS WILD-TYPE           0      15        7       10       10         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16Q LOSS MUTATED           2         0         0          1          3
  16Q LOSS WILD-TYPE         3         2         4          2          7
                    vv
clus                 STAGE IIIC STAGE IV
  16Q LOSS MUTATED            3        0
  16Q LOSS WILD-TYPE         15        3
D62V7, multiclass

Clustering(63) Variable = 17p loss mutation analysis
D63V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   11  6
  17P LOSS WILD-TYPE 16 26
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                17                 42 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 6                 26 
$`17P LOSS MUTATED`
TCGA-D3-A2J6 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A3F3 TCGA-EE-A185 
       10.26        48.79        35.80        51.12         7.00         4.27 
TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
       37.97         4.41         1.08         9.99         6.48         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-FR-A3YN TCGA-FS-A4F9 TCGA-FW-A3R5 
       25.28        23.90         5.95        10.78         1.02 

$`17P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J8 
       16.47        32.55        98.76        28.08        22.55         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A3F8 
        4.01         2.86        13.68        22.36        17.56        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29D 
       11.57         6.31         1.12        12.20         5.13        11.15 
TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A0 TCGA-EE-A2A6 
       38.63         9.47        12.03         8.84        11.31         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-FR-A44A TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       72.16        31.33        84.72        16.21        15.39        14.70 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              1.02               1.12 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             51.12              98.76 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              9.99              14.19 
[1] "1.0 - 51.1 (10.0)" "1.1 - 98.8 (14.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "17P LOSS MUTATED" "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-FR-A3YN 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "17P LOSS MUTATED" "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-FR-A3YN 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "17P LOSS MUTATED" "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-FR-A3YN 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D63V2, continuous
D63V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      9   19
  17P LOSS WILD-TYPE   26   58
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                9                 26
  MALE                 19                 58
                    vv
clus                 M0 M1 M1B M1C
  17P LOSS MUTATED   26  0   1   1
  17P LOSS WILD-TYPE 72  1   1   0
D63V4, multiclass
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0                26                 72
  M1                 0                  1
  M1B                1                  1
  M1C                1                  0
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  17P LOSS MUTATED   15  0   0   2  1   1   2   1  5  1
  17P LOSS WILD-TYPE 46  1   3   8  0   2   6   0  8  1
D63V5, multiclass
D63V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17P LOSS MUTATED             0       3        3        4        1         2
  17P LOSS WILD-TYPE           1      12        4        7       12         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17P LOSS MUTATED           2         0         1          1          4
  17P LOSS WILD-TYPE         3         2         3          2          6
                    vv
clus                 STAGE IIIC STAGE IV
  17P LOSS MUTATED            4        1
  17P LOSS WILD-TYPE         14        2
D63V7, multiclass

Clustering(64) Variable = 17q loss mutation analysis
D64V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    4  4
  17Q LOSS WILD-TYPE 23 28
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                 51 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                 28 
$`17Q LOSS MUTATED`
TCGA-D3-A2J6 TCGA-DA-A1HW TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29X TCGA-ER-A19L 
       10.26        35.80        37.97         4.41         8.09        12.99 
TCGA-FS-A4F9 TCGA-FW-A3R5 
       10.78         1.02 

$`17Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J8 
       16.47        32.55        98.76        28.08        22.55         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB 
        4.01         2.86        48.79        51.12        13.68        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        7.00        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L 
       12.20         4.27         5.13        11.15        38.63         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A0 
        9.47        12.03         8.84         9.99         6.48        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M 
       25.28        23.90         8.94        11.11         4.18        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-GN-A264 TCGA-GN-A265 
       42.84        78.44         5.95        72.16        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       16.21        15.39        14.70 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              1.02               1.08 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             37.97              98.76 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             10.52              13.68 
[1] "1.0 - 38.0 (10.5)" "1.1 - 98.8 (13.7)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"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-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"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-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"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-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D64V2, continuous
D64V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      5    8
  17Q LOSS WILD-TYPE   30   69
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                5                 30
  MALE                  8                 69
                    vv
clus                 M0 M1 M1B M1C
  17Q LOSS MUTATED   11  0   0   1
  17Q LOSS WILD-TYPE 87  1   2   0
D64V4, multiclass
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                11                 87
  M1                 0                  1
  M1B                0                  2
  M1C                1                  0
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  17Q LOSS MUTATED    7  0   0   1  1   1   0   1  1  0
  17Q LOSS WILD-TYPE 54  1   3   9  0   2   8   0 12  2
D64V5, multiclass
D64V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17Q LOSS MUTATED             0       1        2        2        0         1
  17Q LOSS WILD-TYPE           1      14        5        9       13         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17Q LOSS MUTATED           1         0         1          1          1
  17Q LOSS WILD-TYPE         4         2         3          2          9
                    vv
clus                 STAGE IIIC STAGE IV
  17Q LOSS MUTATED            1        1
  17Q LOSS WILD-TYPE         17        2
D64V7, multiclass

Clustering(65) Variable = 18p loss mutation analysis
D65V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    3  5
  18P LOSS WILD-TYPE 24 27
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 8                 51 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 27 
$`18P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3C6 TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A3F5 TCGA-EE-A29D 
       16.47        15.25        48.79        13.68        17.56        11.15 
TCGA-EE-A29T TCGA-EE-A29X 
        6.48         8.09 

$`18P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       32.55        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 
       21.14        11.41         6.35        13.32        24.00         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 
        2.86        35.80        51.12        22.36         7.00        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
       11.57         6.31         1.12        12.20         4.27         5.13 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       37.97        38.63         4.41         1.08         9.47        12.03 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        8.84         9.99        11.31        25.28        23.90         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 
        5.95        72.16        10.78         1.02        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       16.21        15.39        14.70 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              6.48               1.02 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             48.79              98.76 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            14.465             12.200 
[1] "6.5 - 48.8 (14.5)" "1.0 - 98.8 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D65V2, continuous
D65V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     10    8
  18P LOSS WILD-TYPE   25   69
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               10                 25
  MALE                  8                 69
                    vv
clus                 M0 M1 M1B M1C
  18P LOSS MUTATED   18  0   0   0
  18P LOSS WILD-TYPE 80  1   2   1
D65V4, multiclass
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                18                 80
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  18P LOSS MUTATED    9  0   1   1  0   1   2   0  2  2
  18P LOSS WILD-TYPE 52  1   2   9  1   2   6   1 11  0
D65V5, multiclass
D65V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18P LOSS MUTATED             0       1        2        2        4         0
  18P LOSS WILD-TYPE           1      14        5        9        9         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18P LOSS MUTATED           0         0         0          1          2
  18P LOSS WILD-TYPE         5         2         4          2          8
                    vv
clus                 STAGE IIIC STAGE IV
  18P LOSS MUTATED            4        0
  18P LOSS WILD-TYPE         14        3
D65V7, multiclass

Clustering(66) Variable = 18q loss mutation analysis
D66V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    3  7
  18Q LOSS WILD-TYPE 24 25
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                10                 49 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                 25 
$`18Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-DA-A1HV TCGA-DA-A1I2 
       16.47        22.55        15.25        13.32        48.79        13.68 
TCGA-DA-A3F5 TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29X 
       17.56        11.15         6.48         8.09 

$`18Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        10.26         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW 
       11.41         6.35        24.00         4.01         2.86        35.80 
TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       51.12        22.36         7.00        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E 
        1.12        12.20         4.27         5.13        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
        4.41         1.08         9.47        12.03         8.84         9.99 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J 
       11.31        25.28        23.90         8.94        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A 
       12.99        28.64        42.84        78.44         5.95        72.16 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       10.78         1.02        31.33        84.72        16.21        15.39 
TCGA-GN-A26D 
       14.70 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              6.48               1.02 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             48.79              98.76 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            14.465             12.030 
[1] "6.5 - 48.8 (14.5)" "1.0 - 98.8 (12.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D66V2, continuous
D66V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      9    9
  18Q LOSS WILD-TYPE   26   68
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                9                 26
  MALE                  9                 68
                    vv
clus                 M0 M1 M1B M1C
  18Q LOSS MUTATED   17  0   1   0
  18Q LOSS WILD-TYPE 81  1   1   1
D66V4, multiclass
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0                17                 81
  M1                 0                  1
  M1B                1                  1
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  18Q LOSS MUTATED    7  0   1   2  0   2   2   0  3  1
  18Q LOSS WILD-TYPE 54  1   2   8  1   1   6   1 10  1
D66V5, multiclass
D66V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18Q LOSS MUTATED             0       0        2        2        3         0
  18Q LOSS WILD-TYPE           1      15        5        9       10         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18Q LOSS MUTATED           0         0         1          1          3
  18Q LOSS WILD-TYPE         5         2         3          2          7
                    vv
clus                 STAGE IIIC STAGE IV
  18Q LOSS MUTATED            4        0
  18Q LOSS WILD-TYPE         14        3
D66V7, multiclass

Clustering(67) Variable = 19p loss mutation analysis
D67V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    3  5
  19P LOSS WILD-TYPE 24 27
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 8                 51 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                 27 
$`19P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-EE-A29H 
       16.47        22.55         2.86        48.79        35.80         4.41 
TCGA-EE-A29X TCGA-EE-A2A0 
        8.09        11.31 

$`19P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        10.26         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 
       11.41         6.35        15.25        13.32        24.00         4.01 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       51.12        13.68        22.36         7.00        17.56        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
       11.57         6.31         1.12        12.20         4.27         5.13 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       37.97        11.15        38.63         1.08         9.47        12.03 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        8.84         9.99         6.48        25.28        23.90         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 
        5.95        72.16        10.78         1.02        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       16.21        15.39        14.70 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              2.86               1.02 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             48.79              98.76 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             13.89              12.99 
[1] "2.9 - 48.8 (13.9)" "1.0 - 98.8 (13.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D67V2, continuous
D67V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      8    4
  19P LOSS WILD-TYPE   27   73
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                8                 27
  MALE                  4                 73
                    vv
clus                 M0 M1 M1B M1C
  19P LOSS MUTATED   10  0   1   1
  19P LOSS WILD-TYPE 88  1   1   0
D67V4, multiclass
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                10                 88
  M1                 0                  1
  M1B                1                  1
  M1C                1                  0
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  19P LOSS MUTATED    3  0   1   2  0   1   2   1  2  0
  19P LOSS WILD-TYPE 58  1   2   8  1   2   6   0 11  2
D67V5, multiclass
D67V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19P LOSS MUTATED             0       0        1        1        0         1
  19P LOSS WILD-TYPE           1      15        6       10       13         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19P LOSS MUTATED           0         0         1          0          5
  19P LOSS WILD-TYPE         5         2         3          3          5
                    vv
clus                 STAGE IIIC STAGE IV
  19P LOSS MUTATED            1        1
  19P LOSS WILD-TYPE         17        2
D67V7, multiclass

Clustering(68) Variable = 19q loss mutation analysis
D68V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    5  2
  19Q LOSS WILD-TYPE 22 30
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 7                 52 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 30 
$`19Q LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-EE-A29H TCGA-EE-A29S TCGA-EE-A29X 
       22.55         2.86        48.79         4.41         9.99         8.09 
TCGA-GN-A26D 
       14.70 

$`19Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        32.55        98.76        28.08        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 
        4.01        35.80        51.12        13.68        22.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L 
        4.27         5.13        37.97        11.15        38.63         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.47        12.03         8.84         6.48        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       23.90         8.94        11.11         4.18        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 
       42.84        78.44         5.95        72.16        10.78         1.02 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       31.33        84.72        16.21        15.39 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              2.86               1.02 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             48.79              98.76 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             9.990             13.155 
[1] "2.9 - 48.8 (10.0)" "1.0 - 98.8 (13.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-DA-A1HV         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
[1] "hr=" "1.6"
D68V2, continuous
D68V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6    6
  19Q LOSS WILD-TYPE   29   71
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                6                 29
  MALE                  6                 71
                    vv
clus                 M0 M1 M1B M1C
  19Q LOSS MUTATED    8  0   1   1
  19Q LOSS WILD-TYPE 90  1   1   0
D68V4, multiclass
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                 8                 90
  M1                 0                  1
  M1B                1                  1
  M1C                1                  0
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  19Q LOSS MUTATED    4  0   1   1  0   1   2   1  1  0
  19Q LOSS WILD-TYPE 57  1   2   9  1   2   6   0 12  2
D68V5, multiclass
D68V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19Q LOSS MUTATED             0       0        1        1        0         1
  19Q LOSS WILD-TYPE           1      15        6       10       13         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19Q LOSS MUTATED           0         1         1          0          4
  19Q LOSS WILD-TYPE         5         1         3          3          6
                    vv
clus                 STAGE IIIC STAGE IV
  19Q LOSS MUTATED            0        1
  19Q LOSS WILD-TYPE         18        2
D68V7, multiclass

Clustering(69) Variable = 20p loss mutation analysis
D69V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    2  1
  20P LOSS WILD-TYPE 25 31
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 56 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 31 
$`20P LOSS MUTATED`
TCGA-D3-A3CF TCGA-DA-A1HV TCGA-EE-A29E 
       24.00        48.79        38.63 

$`20P LOSS 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-A3CE 
        8.38        21.14        11.41         6.35        15.25        13.32 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB 
        4.01         2.86        35.80        51.12        13.68        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        7.00        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
       12.20         4.27         5.13        37.97        11.15         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        1.08         9.47        12.03         8.84         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F 
        8.09        11.31        25.28        23.90         8.94        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN 
        4.18        12.99        28.64        42.84        78.44         5.95 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       72.16        10.78         1.02        31.33        84.72        16.21 
TCGA-GN-A268 TCGA-GN-A26D 
       15.39        14.70 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             24.00               1.02 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             48.79              98.76 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            38.630             12.115 
[1] "24.0 - 48.8 (38.6)" "1.0 - 98.8 (12.1)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
  "20P LOSS MUTATED" "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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
  "20P LOSS MUTATED" "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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
  "20P LOSS MUTATED" "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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         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-FR-A3YN 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
[1] "hr=" "3.7"
D69V2, continuous
D69V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2    1
  20P LOSS WILD-TYPE   33   76
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                2                 33
  MALE                  1                 76
                    vv
clus                 M0 M1 M1B M1C
  20P LOSS MUTATED    3  0   0   0
  20P LOSS WILD-TYPE 95  1   2   1
D69V4, multiclass
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                 3                 95
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  20P LOSS MUTATED    0  0   0   1  0   0   1   0  1  0
  20P LOSS WILD-TYPE 61  1   3   9  1   3   7   1 12  2
D69V5, multiclass
D69V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  20P LOSS MUTATED             0       0        0        0        0         0
  20P LOSS WILD-TYPE           1      15        7       11       13         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  20P LOSS MUTATED           0         0         0          0          2
  20P LOSS WILD-TYPE         5         2         4          3          8
                    vv
clus                 STAGE IIIC STAGE IV
  20P LOSS MUTATED            1        0
  20P LOSS WILD-TYPE         17        3
D69V7, multiclass

Clustering(70) Variable = 21q loss mutation analysis
D70V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    3  3
  21Q LOSS WILD-TYPE 24 29
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 53 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 29 
$`21Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-EE-A181 TCGA-EE-A29H TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-GN-A268 
       32.55         1.12         4.41        23.90         8.94        15.39 

$`21Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       22.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       12.20         4.27         5.13        37.97        11.15        38.63 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        1.08         9.47        12.03         8.84         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
        8.09        11.31        25.28        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 
       28.64        42.84        78.44         5.95        72.16        10.78 
TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26D 
        1.02        31.33        84.72        16.21        14.70 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              1.12               1.02 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             32.55              98.76 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            12.165             12.990 
[1] "1.1 - 32.5 (12.2)" "1.0 - 98.8 (13.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"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-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "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-FR-A3YN 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"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-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "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-FR-A3YN 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"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-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "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-FR-A3YN 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D70V2, continuous
D70V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5   10
  21Q LOSS WILD-TYPE   30   67
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                5                 30
  MALE                 10                 67
                    vv
clus                 M0 M1 M1B M1C
  21Q LOSS MUTATED   15  0   0   0
  21Q LOSS WILD-TYPE 83  1   2   1
D70V4, multiclass
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0                15                 83
  M1                 0                  1
  M1B                0                  2
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  21Q LOSS MUTATED   12  0   1   1  0   0   1   0  0  0
  21Q LOSS WILD-TYPE 49  1   2   9  1   3   7   1 13  2
D70V5, multiclass
D70V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  21Q LOSS MUTATED             1       2        3        0        4         0
  21Q LOSS WILD-TYPE           0      13        4       11        9         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  21Q LOSS MUTATED           2         0         0          1          1
  21Q LOSS WILD-TYPE         3         2         4          2          9
                    vv
clus                 STAGE IIIC STAGE IV
  21Q LOSS MUTATED            1        0
  21Q LOSS WILD-TYPE         17        3
D70V7, multiclass

Clustering(71) Variable = 22q loss mutation analysis
D71V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    2  2
  22Q LOSS WILD-TYPE 25 30
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 4                 55 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 2                 30 
$`22Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-DA-A1I2 TCGA-EE-A29C TCGA-EE-A2A6 
       28.08        13.68        37.97         8.94 

$`22Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        32.55        98.76        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1IB 
        4.01         2.86        48.79        35.80        51.12        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        7.00        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       12.20         4.27         5.13        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        1.08         9.47        12.03         8.84         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19F TCGA-ER-A19J 
        8.09        11.31        25.28        23.90        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A 
       12.99        28.64        42.84        78.44         5.95        72.16 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       10.78         1.02        31.33        84.72        16.21        15.39 
TCGA-GN-A26D 
       14.70 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              8.94               1.02 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             37.97              98.76 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             20.88              12.20 
[1] "8.9 - 38.0 (20.9)" "1.0 - 98.8 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"22Q LOSS WILD-TYPE"   "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-FR-A3YN 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"22Q LOSS WILD-TYPE"   "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-FR-A3YN 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2J9         TCGA-D3-A2JD 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D9-A3Z1         TCGA-D9-A3Z3 
"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-A1I2         TCGA-DA-A1IB         TCGA-DA-A3F3 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A17X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A181         TCGA-EE-A183 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-ER-A19F 
"22Q LOSS WILD-TYPE"   "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-FR-A3YN 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FR-A44A         TCGA-FS-A4F9         TCGA-FW-A3R5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D71V2, continuous
D71V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2    5
  22Q LOSS WILD-TYPE   33   72
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                2                 33
  MALE                  5                 72
                    vv
clus                 M0 M1 M1B M1C
  22Q LOSS MUTATED    6  0   1   0
  22Q LOSS WILD-TYPE 92  1   1   1
D71V4, multiclass
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0                 6                 92
  M1                 0                  1
  M1B                1                  1
  M1C                0                  1
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  22Q LOSS MUTATED    5  0   0   0  0   0   1   0  1  0
  22Q LOSS WILD-TYPE 56  1   3  10  1   3   7   1 12  2
D71V5, multiclass
D71V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  22Q LOSS MUTATED             0       2        1        2        0         0
  22Q LOSS WILD-TYPE           1      13        6        9       13         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  22Q LOSS MUTATED           0         0         0          0          0
  22Q LOSS WILD-TYPE         5         2         4          3         10
                    vv
clus                 STAGE IIIC STAGE IV
  22Q LOSS MUTATED            1        1
  22Q LOSS WILD-TYPE         17        2
D71V7, multiclass

Clustering(72) Variable = Xq loss mutation analysis
D72V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    1  1
  XQ LOSS WILD-TYPE 26 31
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                57 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                31 
$`XQ LOSS MUTATED`
TCGA-D3-A3C6 TCGA-EE-A29H 
       15.25         4.41 

$`XQ LOSS 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-A3CE TCGA-D3-A3CF 
        8.38        21.14        11.41         6.35        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       22.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
        1.12        12.20         4.27         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
       38.63         1.08         9.47        12.03         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-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-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 
        5.95        72.16        10.78         1.02        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       16.21        15.39        14.70 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             4.41              1.02 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            15.25             98.76 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             9.83             12.99 
[1] "4.4 - 15.2 (9.8)"  "1.0 - 98.8 (13.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A3CF        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"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-FR-A3YN        TCGA-FR-A44A 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FW-A3R5        TCGA-GN-A264        TCGA-GN-A265 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                57 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3CE        TCGA-D3-A3CF 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV        TCGA-DA-A1HW 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1HY        TCGA-DA-A1I2        TCGA-DA-A1IB        TCGA-DA-A3F3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20F 
"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-A29L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29R        TCGA-EE-A29S 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29T        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-A2A6        TCGA-ER-A19F        TCGA-ER-A19J 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N        TCGA-ER-A1A1 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FR-A3YN        TCGA-FR-A44A        TCGA-FS-A4F9        TCGA-FW-A3R5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A267        TCGA-GN-A268 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A26D 
"XQ LOSS WILD-TYPE" 
D72V2, continuous
D72V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    0
  XQ LOSS WILD-TYPE   32   77
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               3                32
  MALE                 0                77
                   vv
clus                M0 M1 M1B M1C
  XQ LOSS MUTATED    3  0   0   0
  XQ LOSS WILD-TYPE 95  1   2   1
D72V4, multiclass
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0                3                95
  M1                0                 1
  M1B               0                 2
  M1C               0                 1
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  XQ LOSS MUTATED    3  0   0   0  0   0   0   0  0  0
  XQ LOSS WILD-TYPE 58  1   3  10  1   3   8   1 13  2
D72V5, multiclass
D72V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  XQ LOSS MUTATED             0       1        1        1        0         0
  XQ LOSS WILD-TYPE           1      14        6       10       13         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  XQ LOSS MUTATED           0         0         0          0          0
  XQ LOSS WILD-TYPE         5         2         4          3         10
                   vv
clus                STAGE IIIC STAGE IV
  XQ LOSS MUTATED            0        0
  XQ LOSS WILD-TYPE         18        3
D72V7, multiclass
                   V1.D                      V2                      V3 
        "Time to Death"                   "AGE"                "GENDER" 
                     V4                      V5                      V6 
   "DISTANT.METASTASIS" "LYMPH.NODE.METASTASIS"       "TUMOR.STAGECODE" 
                     V7 
"NEOPLASM.DISEASESTAGE" 
> q(save="no")
