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

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/19/CNV2ClinicalAnalysis_nozzle_onlysig_arm.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/19/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/SKCM-BRAF_Hotspot_Mutants/3164349/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-BRAF_Hotspot_Mutants/3215663/SKCM-BRAF_Hotspot_Mutants.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-BRAF_Hotspot_Mutants", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"                           "-oT=SKCM-BRAF_Hotspot_Mutants"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=67, in cluster file=99, common to both=67
[1] "Reduce the number of clustering variables from 80 to 70."
[1] 70 67
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3                64 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3                64 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               16                51 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               16                51 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                61 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                61 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                61 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                61 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                63 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                63 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                62 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                62 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                62 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                62 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5                62 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5                62 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                60 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                60 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               15                52 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               15                52 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5                62 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5                62 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               40                27 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               40                27 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               44                23 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               44                23 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12                55 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12                55 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               23                44 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               23                44 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 62 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 62 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 64 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 64 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                11                 56 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                11                 56 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                 62 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                 62 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                 59 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                 59 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 5                 62 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 5                 62 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                 56 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                 56 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 62 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 62 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 61 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 61 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 7                 60 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 7                 60 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 6                 61 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 6                 61 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                10                 57 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                10                 57 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 63 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 63 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                 61 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                 61 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                 60 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                 60 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                24                 43 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                24                 43 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                28                 39 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                28                 39 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 63 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 63 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                17                 50 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                17                 50 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                61 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                61 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                63 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                63 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7                60 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7                60 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                7                60 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                7                60 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                58 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                58 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9                58 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9                58 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                4                63 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                4                63 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                63 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                63 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9                58 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9                58 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               20                47 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               20                47 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                61 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                61 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               31                36 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               31                36 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                7                60 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                7                60 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               38                29 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               38                29 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               29                38 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               29                38 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                36                 31 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                36                 31 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                45                 22 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                45                 22 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                13                 54 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                13                 54 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                15                 52 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                15                 52 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                 64 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                 64 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 63 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 63 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                10                 57 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                10                 57 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                18                 49 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                18                 49 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 61 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 61 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                 62 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                 62 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                 57 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                 57 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                12                 55 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                12                 55 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 62 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 62 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                16                 51 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                16                 51 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                17                 50 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                17                 50 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 6                 61 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 6                 61 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 8                 59 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 8                 59 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 64 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 64 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                 59 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                 59 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 4                 63 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 4                 63 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                63 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                63 
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "DAYSTOSUBMITTEDSPECIMENDX"             
 [5] "VITALSTATUS"                           
 [6] "DCCUPLOADDATE"                         
 [7] "PRIMARYSITEOFDESEASE"                  
 [8] "GENDER"                                
 [9] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[10] "RADIATIONTHERAPY"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "TUMOR.STAGECODE"                       
[15] "NEOPLASM.DISEASESTAGE"                 
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 67 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
          NA           NA         3687           NA           NA           NA 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX 
          NA           NA           NA           NA         4511          194 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
          NA         3564           NA           NA           NA         3265 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
        1861           NA         6553          477           NA         3335 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
        2399           NA           NA         1455         1205          979 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
        1349         1716        10523         1787         1446         4134 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
        5536         1691          595           NA         3931           NA 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP 
          NA           NA           NA           NA         4403         7562 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J 
        3733          112           NA          714           NA           NA 
TCGA-ER-A19O TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
          NA           NA         3080           NA         4525         3664 
TCGA-GN-A265 
        2577 
Variable 1:'AGE':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
[3] "GENDER"                  "DISTANT.METASTASIS"     
[5] "LYMPH.NODE.METASTASIS"   "TUMOR.STAGECODE"        
[7] "NEOPLASM.DISEASESTAGE"  
[1] "TUMOR.?STAGE" "6"           
[1] "stage2"
vv
 T0  T1 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 T4A T4B TIS  TX 
  2   1   5   1  11   6   2   2   7   3   1   2  10   1   7 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 67 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=44, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=9, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED    3  0
  1P GAIN WILD-TYPE 29 34
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3                63 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                0                34 
$`1P GAIN MUTATED`
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2GS 
       39.62        44.35        55.59 

$`1P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX 
       12.10        58.03        60.23         9.30       148.31         6.38 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.17        20.38       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
       61.18        53.92       215.44        15.68        26.86       109.64 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29P 
       78.87       168.26        63.32        47.84        32.19        56.42 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GT 
      345.96        58.75        47.54       135.91       182.01        19.56 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67       129.24        28.80        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF 
       16.96       144.76       248.61       122.73         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
       23.47       138.77         6.41        48.59       228.59         7.76 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR 
      357.37        53.52        15.45        32.71       101.26        11.41 
TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
      148.77       120.46        84.72 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            39.62              3.68 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            55.59            357.37 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            44.35             58.03 
[1] "39.6 - 55.6 (44.4)" "3.7 - 357.4 (58.0)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
[1] "hr="     "2.6e+07"
D1V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1P GAIN MUTATED                    0             1
  1P GAIN WILD-TYPE                  6             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1P GAIN MUTATED                                                                                          0
  1P GAIN WILD-TYPE                                                                                       12
                   vv
clus                REGIONAL LYMPH NODE
  1P GAIN MUTATED                     2
  1P GAIN WILD-TYPE                  46
D1V3, multiclass
                                                                                          clus
vv                                                                                         1P GAIN MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         1P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                12
  REGIONAL LYMPH NODE                                                                                     46
D1V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2    1
  1P GAIN WILD-TYPE   20   44
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               2                20
  MALE                 1                44
                   vv
clus                M0 M1 M1A M1B M1C
  1P GAIN MUTATED    3  0   0   0   0
  1P GAIN WILD-TYPE 53  1   1   1   2
D1V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  1P GAIN MUTATED    2  0   0   1   0   0   0  0  0
  1P GAIN WILD-TYPE 31  1   2   6   1   5   3  7  2
D1V6, multiclass
D1V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1P GAIN MUTATED             0       0        0        2        0         0
  1P GAIN WILD-TYPE           2      10        2        3        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P GAIN MUTATED           0         0          0          1          0
  1P GAIN WILD-TYPE         2         5          2          6          9
                   vv
clus                STAGE IV
  1P GAIN MUTATED          0
  1P GAIN WILD-TYPE        3
D1V8, multiclass

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    9  7
  1Q GAIN WILD-TYPE 23 27
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               16                50 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                7                27 
$`1Q GAIN MUTATED`
TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-EE-A20B 
       11.87        60.23         9.30        35.93       107.34       109.64 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2M7 
       39.62        44.35        58.75       182.01        55.59        28.80 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-FS-A1ZC TCGA-FS-A1ZF 
      122.73         3.68       357.37        15.45 

$`1Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JK 
      112.54        71.80       121.22        31.59        23.77        12.10 
TCGA-D3-A3C6 TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       58.03       148.31         6.38        36.03       117.17        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 
      176.55        61.18        53.92       215.44        15.68        26.86 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29P 
       78.87       168.26        63.32        47.84        32.19        56.42 
TCGA-EE-A29T TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
      345.96        47.54       135.91        19.56        21.67       129.24 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP 
       19.76       103.27       103.17        16.96       144.76       248.61 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY 
       13.81        23.47       138.77         6.41        48.59       228.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
        7.76        53.52        32.71       101.26        11.41       148.77 
TCGA-GN-A262 TCGA-GN-A265 
      120.46        84.72 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             3.68              6.38 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           357.37            345.96 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           49.970            57.225 
[1] "3.7 - 357.4 (50.0)" "6.4 - 346.0 (57.2)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D2V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1Q GAIN MUTATED                    3             1
  1Q GAIN WILD-TYPE                  3             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1Q GAIN MUTATED                                                                                          3
  1Q GAIN WILD-TYPE                                                                                        9
                   vv
clus                REGIONAL LYMPH NODE
  1Q GAIN MUTATED                     9
  1Q GAIN WILD-TYPE                  39
D2V3, multiclass
                                                                                          clus
vv                                                                                         1Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     3
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    9
                                                                                          clus
vv                                                                                         1Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       3
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 9
  REGIONAL LYMPH NODE                                                                                     39
D2V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6   10
  1Q GAIN WILD-TYPE   16   35
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               6                16
  MALE                10                35
                   vv
clus                M0 M1 M1A M1B M1C
  1Q GAIN MUTATED   13  0   0   0   1
  1Q GAIN WILD-TYPE 43  1   1   1   1
D2V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  1Q GAIN MUTATED    9  0   0   3   0   1   1  0  0
  1Q GAIN WILD-TYPE 24  1   2   4   1   4   2  7  2
D2V6, multiclass
D2V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1Q GAIN MUTATED             1       1        1        2        2         0
  1Q GAIN WILD-TYPE           1       9        1        3        6         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q GAIN MUTATED           1         2          0          2          1
  1Q GAIN WILD-TYPE         1         3          2          5          8
                   vv
clus                STAGE IV
  1Q GAIN MUTATED          1
  1Q GAIN WILD-TYPE        2
D2V8, multiclass

Clustering(3) Variable = 2p gain mutation analysis
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    0  6
  2P GAIN WILD-TYPE 32 28
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                60 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                28 
$`2P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-EE-A20H TCGA-EE-A29A TCGA-FS-A1ZD 
       71.80        31.59        11.87       168.26        63.32        53.52 

$`2P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
      112.54       121.22        23.77        12.10        58.03        60.23 
TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.30       148.31         6.38        36.03       117.17        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
      176.55        35.93       107.34        61.18        53.92       215.44 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E 
       15.68        26.86       109.64        78.87        47.84        39.62 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB 
       32.19        44.35        56.42       345.96        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
      135.91       182.01        55.59        19.56        21.67       129.24 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.80        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      248.61       122.73         3.68        13.81        23.47       138.77 
TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZF 
        6.41        48.59       228.59         7.76       357.37        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       32.71       101.26        11.41       148.77       120.46        84.72 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            11.87              3.68 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           168.26            357.37 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           58.420            56.005 
[1] "11.9 - 168.3 (58.4)" "3.7 - 357.4 (56.0)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
[1] "hr=" "2.4"
D3V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2P GAIN MUTATED                    2             0
  2P GAIN WILD-TYPE                  4             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2P GAIN MUTATED                                                                                          1
  2P GAIN WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  2P GAIN MUTATED                     3
  2P GAIN WILD-TYPE                  45
D3V3, multiclass
                                                                                          clus
vv                                                                                         2P GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         2P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       4
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     45
D3V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0    6
  2P GAIN WILD-TYPE   22   39
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               0                22
  MALE                 6                39
                   vv
clus                M0 M1 M1A M1B M1C
  2P GAIN MUTATED    6  0   0   0   0
  2P GAIN WILD-TYPE 50  1   1   1   2
D3V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  2P GAIN MUTATED    2  0   1   2   1   0   0  0  0
  2P GAIN WILD-TYPE 31  1   1   5   0   5   3  7  2
D3V6, multiclass
D3V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2P GAIN MUTATED             0       1        0        0        0         1
  2P GAIN WILD-TYPE           2       9        2        5        8         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P GAIN MUTATED           0         1          1          1          1
  2P GAIN WILD-TYPE         2         4          1          6          8
                   vv
clus                STAGE IV
  2P GAIN MUTATED          0
  2P GAIN WILD-TYPE        3
D3V8, multiclass

Clustering(4) Variable = 2q gain mutation analysis
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    0  6
  2Q GAIN WILD-TYPE 32 28
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                60 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                28 
$`2Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-EE-A20H TCGA-EE-A29A TCGA-FS-A1ZD 
       71.80        31.59        11.87       168.26        63.32        53.52 

$`2Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
      112.54       121.22        23.77        12.10        58.03        60.23 
TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.30       148.31         6.38        36.03       117.17        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
      176.55        35.93       107.34        61.18        53.92       215.44 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E 
       15.68        26.86       109.64        78.87        47.84        39.62 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB 
       32.19        44.35        56.42       345.96        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
      135.91       182.01        55.59        19.56        21.67       129.24 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.80        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      248.61       122.73         3.68        13.81        23.47       138.77 
TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZF 
        6.41        48.59       228.59         7.76       357.37        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       32.71       101.26        11.41       148.77       120.46        84.72 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            11.87              3.68 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           168.26            357.37 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           58.420            56.005 
[1] "11.9 - 168.3 (58.4)" "3.7 - 357.4 (56.0)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
[1] "hr=" "2.4"
D4V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2Q GAIN MUTATED                    2             0
  2Q GAIN WILD-TYPE                  4             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2Q GAIN MUTATED                                                                                          1
  2Q GAIN WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  2Q GAIN MUTATED                     3
  2Q GAIN WILD-TYPE                  45
D4V3, multiclass
                                                                                          clus
vv                                                                                         2Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         2Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       4
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     45
D4V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0    6
  2Q GAIN WILD-TYPE   22   39
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               0                22
  MALE                 6                39
                   vv
clus                M0 M1 M1A M1B M1C
  2Q GAIN MUTATED    6  0   0   0   0
  2Q GAIN WILD-TYPE 50  1   1   1   2
D4V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  2Q GAIN MUTATED    2  0   1   2   1   0   0  0  0
  2Q GAIN WILD-TYPE 31  1   1   5   0   5   3  7  2
D4V6, multiclass
D4V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2Q GAIN MUTATED             0       1        0        0        0         1
  2Q GAIN WILD-TYPE           2       9        2        5        8         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q GAIN MUTATED           0         1          1          1          1
  2Q GAIN WILD-TYPE         2         4          1          6          8
                   vv
clus                STAGE IV
  2Q GAIN MUTATED          0
  2Q GAIN WILD-TYPE        3
D4V8, multiclass

Clustering(5) Variable = 3p gain mutation analysis
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    3  1
  3P GAIN WILD-TYPE 29 33
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                62 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                33 
$`3P GAIN MUTATED`
TCGA-DA-A3F5 TCGA-EE-A20H TCGA-EE-A29M TCGA-EE-A29T 
      215.44       168.26        44.35       345.96 

$`3P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX 
       12.10        58.03        60.23         9.30       148.31         6.38 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.17        20.38       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       61.18        53.92        15.68        26.86       109.64        78.87 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2A6 
       63.32        47.84        39.62        32.19        56.42        58.75 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       47.54       135.91       182.01        55.59        19.56        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
      129.24        28.80        19.76       103.27       103.17        16.96 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      144.76       248.61       122.73         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC 
      138.77         6.41        48.59       228.59         7.76       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
       53.52        15.45        32.71       101.26        11.41       148.77 
TCGA-GN-A262 TCGA-GN-A265 
      120.46        84.72 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            44.35              3.68 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           345.96            357.37 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
          191.850            54.755 
[1] "44.4 - 346.0 (191.8)" "3.7 - 357.4 (54.8)"  
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "hr=" "4.2"
D5V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3P GAIN MUTATED                    1             1
  3P GAIN WILD-TYPE                  5             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3P GAIN MUTATED                                                                                          0
  3P GAIN WILD-TYPE                                                                                       12
                   vv
clus                REGIONAL LYMPH NODE
  3P GAIN MUTATED                     2
  3P GAIN WILD-TYPE                  46
D5V3, multiclass
                                                                                          clus
vv                                                                                         3P GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         3P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                12
  REGIONAL LYMPH NODE                                                                                     46
D5V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2    2
  3P GAIN WILD-TYPE   20   43
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               2                20
  MALE                 2                43
                   vv
clus                M0 M1 M1A M1B M1C
  3P GAIN MUTATED    4  0   0   0   0
  3P GAIN WILD-TYPE 52  1   1   1   2
D5V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  3P GAIN MUTATED    2  0   0   0   0   0   0  1  1
  3P GAIN WILD-TYPE 31  1   2   7   1   5   3  6  1
D5V6, multiclass
D5V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3P GAIN MUTATED             0       1        0        1        0         0
  3P GAIN WILD-TYPE           2       9        2        4        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3P GAIN MUTATED           0         0          0          0          1
  3P GAIN WILD-TYPE         2         5          2          7          8
                   vv
clus                STAGE IV
  3P GAIN MUTATED          0
  3P GAIN WILD-TYPE        3
D5V8, multiclass

Clustering(6) Variable = 3q gain mutation analysis
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    4  1
  3Q GAIN WILD-TYPE 28 33
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                61 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                33 
$`3Q GAIN MUTATED`
TCGA-DA-A3F5 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29M TCGA-EE-A29T 
      215.44        78.87       168.26        44.35       345.96 

$`3Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX 
       12.10        58.03        60.23         9.30       148.31         6.38 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.17        20.38       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A29A 
       61.18        53.92        15.68        26.86       109.64        63.32 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2A6 TCGA-EE-A2GB 
       47.84        39.62        32.19        56.42        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
      135.91       182.01        55.59        19.56        21.67       129.24 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.80        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      248.61       122.73         3.68        13.81        23.47       138.77 
TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
        6.41        48.59       228.59         7.76       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
       15.45        32.71       101.26        11.41       148.77       120.46 
TCGA-GN-A265 
       84.72 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            44.35              3.68 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           345.96            357.37 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           168.26             53.92 
[1] "44.4 - 346.0 (168.3)" "3.7 - 357.4 (53.9)"  
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
[1] "hr=" "5"  
D6V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3Q GAIN MUTATED                    1             1
  3Q GAIN WILD-TYPE                  5             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3Q GAIN MUTATED                                                                                          0
  3Q GAIN WILD-TYPE                                                                                       12
                   vv
clus                REGIONAL LYMPH NODE
  3Q GAIN MUTATED                     3
  3Q GAIN WILD-TYPE                  45
D6V3, multiclass
                                                                                          clus
vv                                                                                         3Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         3Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                12
  REGIONAL LYMPH NODE                                                                                     45
D6V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2    3
  3Q GAIN WILD-TYPE   20   42
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               2                20
  MALE                 3                42
                   vv
clus                M0 M1 M1A M1B M1C
  3Q GAIN MUTATED    5  0   0   0   0
  3Q GAIN WILD-TYPE 51  1   1   1   2
D6V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  3Q GAIN MUTATED    3  0   0   0   0   0   0  1  1
  3Q GAIN WILD-TYPE 30  1   2   7   1   5   3  6  1
D6V6, multiclass
D6V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3Q GAIN MUTATED             0       1        0        1        1         0
  3Q GAIN WILD-TYPE           2       9        2        4        7         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q GAIN MUTATED           0         0          0          0          1
  3Q GAIN WILD-TYPE         2         5          2          7          8
                   vv
clus                STAGE IV
  3Q GAIN MUTATED          0
  3Q GAIN WILD-TYPE        3
D6V8, multiclass

Clustering(7) Variable = 4p gain mutation analysis
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    4  1
  4P GAIN WILD-TYPE 28 33
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                61 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                33 
$`4P GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A3F5 TCGA-EE-A29P TCGA-EE-A2GB TCGA-FS-A1ZM 
       60.23       215.44        56.42        47.54       101.26 

$`4P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       12.10        58.03         9.30       148.31         6.38        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.17        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       53.92        15.68        26.86       109.64        78.87       168.26 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T 
       63.32        47.84        39.62        32.19        44.35       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       58.75       135.91       182.01        55.59        19.56        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
      129.24        28.80        19.76       103.27       103.17        16.96 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      144.76       248.61       122.73         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC 
      138.77         6.41        48.59       228.59         7.76       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
       53.52        15.45        32.71        11.41       148.77       120.46 
TCGA-GN-A265 
       84.72 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            47.54              3.68 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           215.44            357.37 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            60.23             53.92 
[1] "47.5 - 215.4 (60.2)" "3.7 - 357.4 (53.9)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
[1] "hr=" "3.2"
D7V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4P GAIN MUTATED                    0             0
  4P GAIN WILD-TYPE                  6             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4P GAIN MUTATED                                                                                          1
  4P GAIN WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  4P GAIN MUTATED                     4
  4P GAIN WILD-TYPE                  44
D7V3, multiclass
                                                                                          clus
vv                                                                                         4P GAIN MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         4P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     44
D7V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    3
  4P GAIN WILD-TYPE   20   42
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               2                20
  MALE                 3                42
                   vv
clus                M0 M1 M1A M1B M1C
  4P GAIN MUTATED    5  0   0   0   0
  4P GAIN WILD-TYPE 51  1   1   1   2
D7V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  4P GAIN MUTATED    1  0   1   1   0   0   1  1  0
  4P GAIN WILD-TYPE 32  1   1   6   1   5   2  6  2
D7V6, multiclass
D7V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4P GAIN MUTATED             0       0        0        0        0         0
  4P GAIN WILD-TYPE           2      10        2        5        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P GAIN MUTATED           1         2          1          0          1
  4P GAIN WILD-TYPE         1         3          1          7          8
                   vv
clus                STAGE IV
  4P GAIN MUTATED          0
  4P GAIN WILD-TYPE        3
D7V8, multiclass

Clustering(8) Variable = 4q gain mutation analysis
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    4  1
  4Q GAIN WILD-TYPE 28 33
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5                61 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                33 
$`4Q GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A3F5 TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A3AD 
       60.23       215.44        56.42        47.54         3.68 

$`4Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       12.10        58.03         9.30       148.31         6.38        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.17        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       53.92        15.68        26.86       109.64        78.87       168.26 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T 
       63.32        47.84        39.62        32.19        44.35       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       58.75       135.91       182.01        55.59        19.56        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
      129.24        28.80        19.76       103.27       103.17        16.96 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      144.76       248.61       122.73        13.81        23.47       138.77 
TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
        6.41        48.59       228.59         7.76       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
       15.45        32.71       101.26        11.41       148.77       120.46 
TCGA-GN-A265 
       84.72 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             3.68              6.38 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           215.44            357.37 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            56.42             55.59 
[1] "3.7 - 215.4 (56.4)" "6.4 - 357.4 (55.6)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
[1] "hr=" "2.5"
D8V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4Q GAIN MUTATED                    0             0
  4Q GAIN WILD-TYPE                  6             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4Q GAIN MUTATED                                                                                          0
  4Q GAIN WILD-TYPE                                                                                       12
                   vv
clus                REGIONAL LYMPH NODE
  4Q GAIN MUTATED                     5
  4Q GAIN WILD-TYPE                  43
D8V3, multiclass
                                                                                          clus
vv                                                                                         4Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         4Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                12
  REGIONAL LYMPH NODE                                                                                     43
D8V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    3
  4Q GAIN WILD-TYPE   20   42
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2                20
  MALE                 3                42
                   vv
clus                M0 M1 M1A M1B M1C
  4Q GAIN MUTATED    4  0   0   0   0
  4Q GAIN WILD-TYPE 52  1   1   1   2
D8V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  4Q GAIN MUTATED    1  0   1   1   0   0   0  1  0
  4Q GAIN WILD-TYPE 32  1   1   6   1   5   3  6  2
D8V6, multiclass
D8V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4Q GAIN MUTATED             0       0        0        0        0         0
  4Q GAIN WILD-TYPE           2      10        2        5        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q GAIN MUTATED           1         1          1          0          1
  4Q GAIN WILD-TYPE         1         4          1          7          8
                   vv
clus                STAGE IV
  4Q GAIN MUTATED          0
  4Q GAIN WILD-TYPE        3
D8V8, multiclass

Clustering(9) Variable = 5p gain mutation analysis
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    4  2
  5P GAIN WILD-TYPE 28 32
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                6                60 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                32 
$`5P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D9-A148 TCGA-EE-A20H TCGA-EE-A29T TCGA-EE-A2M6 TCGA-EE-A2MP 
      112.54       148.31       168.26       345.96       129.24       248.61 

$`5P GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       71.80       121.22        31.59        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY 
       58.03        60.23         9.30         6.38        36.03       117.17 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A 
      215.44        15.68        26.86       109.64        78.87        63.32 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A6 
       47.84        39.62        32.19        44.35        56.42        58.75 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       47.54       135.91       182.01        55.59        19.56        21.67 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.80        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J 
      122.73         3.68        13.81        23.47       138.77         6.41 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       48.59       228.59         7.76       357.37        53.52        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       32.71       101.26        11.41       148.77       120.46        84.72 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           112.54              3.68 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           345.96            357.37 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
          158.285            51.055 
[1] "112.5 - 346.0 (158.3)" "3.7 - 357.4 (51.1)"   
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "hr=" "3.5"
D9V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5P GAIN MUTATED                    1             0
  5P GAIN WILD-TYPE                  5             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5P GAIN MUTATED                                                                                          0
  5P GAIN WILD-TYPE                                                                                       12
                   vv
clus                REGIONAL LYMPH NODE
  5P GAIN MUTATED                     6
  5P GAIN WILD-TYPE                  42
D9V3, multiclass
                                                                                          clus
vv                                                                                         5P GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    6
                                                                                          clus
vv                                                                                         5P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                12
  REGIONAL LYMPH NODE                                                                                     42
D9V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    5
  5P GAIN WILD-TYPE   20   40
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               2                20
  MALE                 5                40
                   vv
clus                M0 M1 M1A M1B M1C
  5P GAIN MUTATED    6  0   0   1   0
  5P GAIN WILD-TYPE 50  1   1   0   2
D9V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  5P GAIN MUTATED    4  0   0   1   0   0   0  1  1
  5P GAIN WILD-TYPE 29  1   2   6   1   5   3  6  1
D9V6, multiclass
D9V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5P GAIN MUTATED             1       3        0        0        0         0
  5P GAIN WILD-TYPE           1       7        2        5        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P GAIN MUTATED           0         0          0          1          0
  5P GAIN WILD-TYPE         2         5          2          6          9
                   vv
clus                STAGE IV
  5P GAIN MUTATED          0
  5P GAIN WILD-TYPE        3
D9V8, multiclass

Clustering(10) Variable = 6p gain mutation analysis
D10V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    7  7
  6P GAIN WILD-TYPE 25 27
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               14                52 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7                27 
$`6P GAIN MUTATED`
TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A3C6 TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-EE-A20H 
      121.22        23.77        58.03        20.38       176.55       168.26 
TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GT TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AD 
       56.42       182.01        19.56       144.76       248.61         3.68 
TCGA-EE-A3AF TCGA-FS-A1ZC 
       13.81       357.37 

$`6P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CE 
      112.54        71.80        31.59        11.87        12.10        60.23 
TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I4 
        9.30       148.31         6.38        36.03       117.17        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 
      107.34        61.18        53.92       215.44        15.68        26.86 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
      109.64        78.87        63.32        47.84        39.62        32.19 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GS 
       44.35       345.96        58.75        47.54       135.91        55.59 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67       129.24        28.80        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX 
       16.96       122.73        23.47       138.77         6.41        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM 
      228.59         7.76        53.52        15.45        32.71       101.26 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       11.41       148.77       120.46        84.72 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             3.68              6.38 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           357.37            345.96 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           89.625            53.720 
[1] "3.7 - 357.4 (89.6)" "6.4 - 346.0 (53.7)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D10V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6P GAIN MUTATED                    2             0
  6P GAIN WILD-TYPE                  4             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6P GAIN MUTATED                                                                                          1
  6P GAIN WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  6P GAIN MUTATED                    12
  6P GAIN WILD-TYPE                  36
D10V3, multiclass
                                                                                          clus
vv                                                                                         6P GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                   12
                                                                                          clus
vv                                                                                         6P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       4
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     36
D10V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6    9
  6P GAIN WILD-TYPE   16   36
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               6                16
  MALE                 9                36
                   vv
clus                M0 M1 M1A M1B M1C
  6P GAIN MUTATED   12  0   1   0   0
  6P GAIN WILD-TYPE 44  1   0   1   2
D10V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  6P GAIN MUTATED    9  0   0   1   0   1   0  2  0
  6P GAIN WILD-TYPE 24  1   2   6   1   4   3  5  2
D10V6, multiclass
D10V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6P GAIN MUTATED             1       3        0        2        1         1
  6P GAIN WILD-TYPE           1       7        2        3        7         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P GAIN MUTATED           1         0          0          1          3
  6P GAIN WILD-TYPE         1         5          2          6          6
                   vv
clus                STAGE IV
  6P GAIN MUTATED          0
  6P GAIN WILD-TYPE        3
D10V8, multiclass

Clustering(11) Variable = 6q gain mutation analysis
D11V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    3  2
  6Q GAIN WILD-TYPE 29 32
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5                61 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                32 
$`6Q GAIN MUTATED`
TCGA-D3-A1Q7 TCGA-DA-A1I0 TCGA-EE-A2GH TCGA-EE-A2GT TCGA-FS-A1ZC 
      121.22        20.38       182.01        19.56       357.37 

$`6Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
      112.54        71.80        31.59        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       58.03        60.23         9.30       148.31         6.38        36.03 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      117.17       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
      215.44        15.68        26.86       109.64        78.87       168.26 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       63.32        47.84        39.62        32.19        44.35        56.42 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GS TCGA-EE-A2M5 
      345.96        58.75        47.54       135.91        55.59        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
      129.24        28.80        19.76       103.27       103.17        16.96 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      144.76       248.61       122.73         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZD 
      138.77         6.41        48.59       228.59         7.76        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
       15.45        32.71       101.26        11.41       148.77       120.46 
TCGA-GN-A265 
       84.72 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            19.56              3.68 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           357.37            345.96 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           121.22             55.59 
[1] "19.6 - 357.4 (121.2)" "3.7 - 346.0 (55.6)"  
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
[1] "hr=" "3.9"
D11V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6Q GAIN MUTATED                    1             0
  6Q GAIN WILD-TYPE                  5             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6Q GAIN MUTATED                                                                                          1
  6Q GAIN WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  6Q GAIN MUTATED                     3
  6Q GAIN WILD-TYPE                  45
D11V3, multiclass
                                                                                          clus
vv                                                                                         6Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         6Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     45
D11V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    4
  6Q GAIN WILD-TYPE   21   41
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               1                21
  MALE                 4                41
                   vv
clus                M0 M1 M1A M1B M1C
  6Q GAIN MUTATED    4  0   1   0   0
  6Q GAIN WILD-TYPE 52  1   0   1   2
D11V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  6Q GAIN MUTATED    4  0   0   0   0   0   0  1  0
  6Q GAIN WILD-TYPE 29  1   2   7   1   5   3  6  2
D11V6, multiclass
D11V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6Q GAIN MUTATED             1       1        0        1        0         1
  6Q GAIN WILD-TYPE           1       9        2        4        8         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q GAIN MUTATED           0         0          0          0          1
  6Q GAIN WILD-TYPE         2         5          2          7          8
                   vv
clus                STAGE IV
  6Q GAIN MUTATED          0
  6Q GAIN WILD-TYPE        3
D11V8, multiclass

Clustering(12) Variable = 7p gain mutation analysis
D12V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   18 21
  7P GAIN WILD-TYPE 14 13
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               39                27 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               21                13 
$`7P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3MO TCGA-D9-A1JX 
      112.54        71.80        31.59        11.87         9.30         6.38 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.17        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29P 
       53.92       168.26        63.32        47.84        39.62        56.42 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2M6 
      345.96        58.75        47.54       135.91       182.01       129.24 
TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AF 
       28.80        16.96       144.76       248.61         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       23.47       138.77         6.41         7.76       357.37        53.52 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR 
       32.71       101.26        11.41 

$`7P GAIN WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D9-A148 
      121.22        23.77        12.10        58.03        60.23       148.31 
TCGA-DA-A1HW TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       36.03       215.44        15.68        26.86       109.64        78.87 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 
       32.19        44.35        55.59        19.56        21.67        19.76 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A3AB TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1ZF 
      103.27       103.17       122.73        48.59       228.59        15.45 
TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
      148.77       120.46        84.72 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             3.68             12.10 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           357.37            228.59 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            53.92             58.03 
[1] "3.7 - 357.4 (53.9)"  "12.1 - 228.6 (58.0)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D12V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7P GAIN MUTATED                    4             0
  7P GAIN WILD-TYPE                  2             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7P GAIN MUTATED                                                                                          9
  7P GAIN WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  7P GAIN MUTATED                    27
  7P GAIN WILD-TYPE                  21
D12V3, multiclass
                                                                                          clus
vv                                                                                         7P GAIN MUTATED
  DISTANT METASTASIS                                                                                     4
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               9
  REGIONAL LYMPH NODE                                                                                   27
                                                                                          clus
vv                                                                                         7P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       2
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     21
D12V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9   31
  7P GAIN WILD-TYPE   13   14
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               9                13
  MALE                31                14
                   vv
clus                M0 M1 M1A M1B M1C
  7P GAIN MUTATED   33  1   1   0   2
  7P GAIN WILD-TYPE 23  0   0   1   0
D12V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  7P GAIN MUTATED   17  0   2   5   1   3   3  4  2
  7P GAIN WILD-TYPE 16  1   0   2   0   2   0  3  0
D12V6, multiclass
D12V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  7P GAIN MUTATED             2       5        1        1        5         1
  7P GAIN WILD-TYPE           0       5        1        4        3         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7P GAIN MUTATED           1         3          2          5          6
  7P GAIN WILD-TYPE         1         2          0          2          3
                   vv
clus                STAGE IV
  7P GAIN MUTATED          3
  7P GAIN WILD-TYPE        0
D12V8, multiclass

Clustering(13) Variable = 7q gain mutation analysis
D13V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   20 23
  7Q GAIN WILD-TYPE 12 11
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               43                23 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               23                11 
$`7Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3MO TCGA-D9-A1JX 
      112.54        71.80        31.59        11.87         9.30         6.38 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.17        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29A 
       53.92       215.44        15.68        26.86       168.26        63.32 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB 
       47.84        39.62        56.42       345.96        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2MK 
      135.91       182.01       129.24        28.80        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1Z7 
      248.61        13.81        23.47       138.77         6.41         7.76 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR 
      357.37        53.52        15.45        32.71       101.26        11.41 
TCGA-FS-A1ZS 
      148.77 

$`7Q GAIN WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D9-A148 
      121.22        23.77        12.10        58.03        60.23       148.31 
TCGA-DA-A1HW TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2GS 
       36.03       109.64        78.87        32.19        44.35        55.59 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A3AB 
       19.56        21.67        19.76       103.27       103.17       122.73 
TCGA-EE-A3AD TCGA-FS-A1YX TCGA-FS-A1YY TCGA-GN-A262 TCGA-GN-A265 
        3.68        48.59       228.59       120.46        84.72 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             6.38              3.68 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           357.37            228.59 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            53.92             58.03 
[1] "6.4 - 357.4 (53.9)" "3.7 - 228.6 (58.0)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7Q GAIN MUTATED                    5             0
  7Q GAIN WILD-TYPE                  1             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7Q GAIN MUTATED                                                                                          9
  7Q GAIN WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  7Q GAIN MUTATED                    30
  7Q GAIN WILD-TYPE                  18
D13V3, multiclass
                                                                                          clus
vv                                                                                         7Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     5
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               9
  REGIONAL LYMPH NODE                                                                                   30
                                                                                          clus
vv                                                                                         7Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       1
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     18
D13V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     10   34
  7Q GAIN WILD-TYPE   12   11
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              10                12
  MALE                34                11
                   vv
clus                M0 M1 M1A M1B M1C
  7Q GAIN MUTATED   38  1   1   0   2
  7Q GAIN WILD-TYPE 18  0   0   1   0
D13V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  7Q GAIN MUTATED   20  0   2   5   1   4   3  5  2
  7Q GAIN WILD-TYPE 13  1   0   2   0   1   0  2  0
D13V6, multiclass
D13V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  7Q GAIN MUTATED             2       6        1        1        6         1
  7Q GAIN WILD-TYPE           0       4        1        4        2         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q GAIN MUTATED           2         3          2          6          7
  7Q GAIN WILD-TYPE         0         2          0          1          2
                   vv
clus                STAGE IV
  7Q GAIN MUTATED          3
  7Q GAIN WILD-TYPE        0
D13V8, multiclass

Clustering(14) Variable = 8p gain mutation analysis
D14V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    4  8
  8P GAIN WILD-TYPE 28 26
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12                54 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                8                26 
$`8P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3CE TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 
       71.80        60.23       117.17       176.55        35.93       215.44 
TCGA-EE-A2M6 TCGA-EE-A3AD TCGA-ER-A19J TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZR 
      129.24         3.68         6.41         7.76        53.52        11.41 

$`8P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
      112.54       121.22        31.59        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1I0 
       58.03         9.30       148.31         6.38        36.03        20.38 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
      107.34        61.18        53.92        15.68        26.86       109.64 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       78.87       168.26        63.32        47.84        39.62        32.19 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       44.35        56.42       345.96        58.75        47.54       135.91 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 
      182.01        55.59        19.56        21.67        28.80        19.76 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB 
      103.27       103.17        16.96       144.76       248.61       122.73 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1ZC 
       13.81        23.47       138.77        48.59       228.59       357.37 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       15.45        32.71       101.26       148.77       120.46        84.72 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             3.68              6.38 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           215.44            357.37 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           56.875            56.005 
[1] "3.7 - 215.4 (56.9)" "6.4 - 357.4 (56.0)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D14V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8P GAIN MUTATED                    0             0
  8P GAIN WILD-TYPE                  6             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8P GAIN MUTATED                                                                                          3
  8P GAIN WILD-TYPE                                                                                        9
                   vv
clus                REGIONAL LYMPH NODE
  8P GAIN MUTATED                     9
  8P GAIN WILD-TYPE                  39
D14V3, multiclass
                                                                                          clus
vv                                                                                         8P GAIN MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    9
                                                                                          clus
vv                                                                                         8P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 9
  REGIONAL LYMPH NODE                                                                                     39
D14V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   11
  8P GAIN WILD-TYPE   21   34
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               1                21
  MALE                11                34
                   vv
clus                M0 M1 M1A M1B M1C
  8P GAIN MUTATED   10  1   0   0   0
  8P GAIN WILD-TYPE 46  0   1   1   2
D14V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  8P GAIN MUTATED    3  0   0   3   0   2   0  3  0
  8P GAIN WILD-TYPE 30  1   2   4   1   3   3  4  2
D14V6, multiclass
D14V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8P GAIN MUTATED             0       1        0        0        1         1
  8P GAIN WILD-TYPE           2       9        2        5        7         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P GAIN MUTATED           0         2          0          1          4
  8P GAIN WILD-TYPE         2         3          2          6          5
                   vv
clus                STAGE IV
  8P GAIN MUTATED          1
  8P GAIN WILD-TYPE        2
D14V8, multiclass

Clustering(15) Variable = 8q gain mutation analysis
D15V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   10 13
  8Q GAIN WILD-TYPE 22 21
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               23                43 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               13                21 
$`8Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 
       71.80        31.59        60.23         9.30       117.17        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-EE-A29E TCGA-EE-A29T TCGA-EE-A2GH 
      176.55        35.93       215.44        39.62       345.96       182.01 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A3AB TCGA-EE-A3AD TCGA-ER-A19J TCGA-FS-A1YY 
       55.59       129.24       122.73         3.68         6.41       228.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZR TCGA-FS-A1ZS 
        7.76       357.37        53.52        11.41       148.77 

$`8Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
      112.54       121.22        23.77        11.87        12.10        58.03 
TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      148.31         6.38        36.03       107.34        61.18        53.92 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       15.68        26.86       109.64        78.87       168.26        63.32 
TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A6 TCGA-EE-A2GB 
       47.84        32.19        44.35        56.42        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME 
      135.91        19.56        21.67        28.80        19.76       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AF TCGA-EE-A3AG 
      103.17        16.96       144.76       248.61        13.81        23.47 
TCGA-EE-A3AH TCGA-FS-A1YX TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-GN-A262 
      138.77        48.59        15.45        32.71       101.26       120.46 
TCGA-GN-A265 
       84.72 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             3.68              6.38 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           357.37            248.61 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            60.23             53.92 
[1] "3.7 - 357.4 (60.2)" "6.4 - 248.6 (53.9)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D15V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8Q GAIN MUTATED                    2             0
  8Q GAIN WILD-TYPE                  4             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8Q GAIN MUTATED                                                                                          5
  8Q GAIN WILD-TYPE                                                                                        7
                   vv
clus                REGIONAL LYMPH NODE
  8Q GAIN MUTATED                    16
  8Q GAIN WILD-TYPE                  32
D15V3, multiclass
                                                                                          clus
vv                                                                                         8Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                   16
                                                                                          clus
vv                                                                                         8Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       4
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 7
  REGIONAL LYMPH NODE                                                                                     32
D15V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4   19
  8Q GAIN WILD-TYPE   18   26
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               4                18
  MALE                19                26
                   vv
clus                M0 M1 M1A M1B M1C
  8Q GAIN MUTATED   19  1   1   0   0
  8Q GAIN WILD-TYPE 37  0   0   1   2
D15V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  8Q GAIN MUTATED    8  0   0   4   1   2   1  4  1
  8Q GAIN WILD-TYPE 25  1   2   3   0   3   2  3  1
D15V6, multiclass
D15V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8Q GAIN MUTATED             1       2        0        1        2         2
  8Q GAIN WILD-TYPE           1       8        2        4        6         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q GAIN MUTATED           0         3          0          3          5
  8Q GAIN WILD-TYPE         2         2          2          4          4
                   vv
clus                STAGE IV
  8Q GAIN MUTATED          1
  8Q GAIN WILD-TYPE        2
D15V8, multiclass

Clustering(16) Variable = 11p gain mutation analysis
D16V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    3  2
  11P GAIN WILD-TYPE 29 32
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 61 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 32 
$`11P GAIN MUTATED`
TCGA-D3-A3CE TCGA-EE-A29T TCGA-EE-A2GB TCGA-FS-A1ZD TCGA-FS-A1ZS 
       60.23       345.96        47.54        53.52       148.77 

$`11P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       12.10        58.03         9.30       148.31         6.38        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.17        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       53.92       215.44        15.68        26.86       109.64        78.87 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
      168.26        63.32        47.84        39.62        32.19        44.35 
TCGA-EE-A29P TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT 
       56.42        58.75       135.91       182.01        55.59        19.56 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67       129.24        28.80        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF 
       16.96       144.76       248.61       122.73         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
       23.47       138.77         6.41        48.59       228.59         7.76 
TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-GN-A262 
      357.37        15.45        32.71       101.26        11.41       120.46 
TCGA-GN-A265 
       84.72 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             47.54               3.68 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            345.96             357.37 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             60.23              55.59 
[1] "47.5 - 346.0 (60.2)" "3.7 - 357.4 (55.6)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D16V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11P GAIN MUTATED                    0             0
  11P GAIN WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11P GAIN MUTATED                                                                                          0
  11P GAIN WILD-TYPE                                                                                       12
                    vv
clus                 REGIONAL LYMPH NODE
  11P GAIN MUTATED                     5
  11P GAIN WILD-TYPE                  43
D16V3, multiclass
                                                                                          clus
vv                                                                                         11P GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         11P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 12
  REGIONAL LYMPH NODE                                                                                      43
D16V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    3
  11P GAIN WILD-TYPE   20   42
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                 20
  MALE                  3                 42
                    vv
clus                 M0 M1 M1A M1B M1C
  11P GAIN MUTATED    5  0   0   0   0
  11P GAIN WILD-TYPE 51  1   1   1   2
D16V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  11P GAIN MUTATED    2  0   1   1   0   0   0  0  1
  11P GAIN WILD-TYPE 31  1   1   6   1   5   3  7  1
D16V6, multiclass
D16V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11P GAIN MUTATED             0       0        0        0        1         1
  11P GAIN WILD-TYPE           2      10        2        5        7         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  11P GAIN MUTATED           0         1          1          0          0
  11P GAIN WILD-TYPE         2         4          1          7          9
                    vv
clus                 STAGE IV
  11P GAIN MUTATED          0
  11P GAIN WILD-TYPE        3
D16V8, multiclass

Clustering(17) Variable = 11q gain mutation analysis
D17V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    1  2
  11Q GAIN WILD-TYPE 31 32
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 63 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 32 
$`11Q GAIN MUTATED`
TCGA-D3-A3CE TCGA-FS-A1ZD TCGA-FS-A1ZS 
       60.23        53.52       148.77 

$`11Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       12.10        58.03         9.30       148.31         6.38        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.17        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       53.92       215.44        15.68        26.86       109.64        78.87 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
      168.26        63.32        47.84        39.62        32.19        44.35 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
       56.42       345.96        58.75        47.54       135.91       182.01 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.59        19.56        21.67       129.24        28.80        19.76 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB 
      103.27       103.17        16.96       144.76       248.61       122.73 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX 
        3.68        13.81        23.47       138.77         6.41        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM 
      228.59         7.76       357.37        15.45        32.71       101.26 
TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
       11.41       120.46        84.72 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             53.52               3.68 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            148.77             357.37 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             60.23              55.59 
[1] "53.5 - 148.8 (60.2)" "3.7 - 357.4 (55.6)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D17V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11Q GAIN MUTATED                    0             0
  11Q GAIN WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11Q GAIN MUTATED                                                                                          0
  11Q GAIN WILD-TYPE                                                                                       12
                    vv
clus                 REGIONAL LYMPH NODE
  11Q GAIN MUTATED                     3
  11Q GAIN WILD-TYPE                  45
D17V3, multiclass
                                                                                          clus
vv                                                                                         11Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         11Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 12
  REGIONAL LYMPH NODE                                                                                      45
D17V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    2
  11Q GAIN WILD-TYPE   21   43
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                1                 21
  MALE                  2                 43
                    vv
clus                 M0 M1 M1A M1B M1C
  11Q GAIN MUTATED    3  0   0   0   0
  11Q GAIN WILD-TYPE 53  1   1   1   2
D17V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  11Q GAIN MUTATED    2  0   0   1   0   0   0  0  0
  11Q GAIN WILD-TYPE 31  1   2   6   1   5   3  7  2
D17V6, multiclass
D17V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11Q GAIN MUTATED             0       0        0        0        1         1
  11Q GAIN WILD-TYPE           2      10        2        5        7         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  11Q GAIN MUTATED           0         1          0          0          0
  11Q GAIN WILD-TYPE         2         4          2          7          9
                    vv
clus                 STAGE IV
  11Q GAIN MUTATED          0
  11Q GAIN WILD-TYPE        3
D17V8, multiclass

Clustering(18) Variable = 12p gain mutation analysis
D18V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    6  5
  12P GAIN WILD-TYPE 26 29
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                11                 55 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 5                 29 
$`12P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A20H 
       71.80        31.59        60.23        61.18       215.44       168.26 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2M6 TCGA-ER-A19J TCGA-FS-A1ZM 
       58.75        47.54       129.24         6.41       101.26 

$`12P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
      112.54       121.22        23.77        11.87        12.10        58.03 
TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.30       148.31         6.38        36.03       117.17        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 
      176.55        35.93       107.34        53.92        15.68        26.86 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
      109.64        78.87        63.32        47.84        39.62        32.19 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS 
       44.35        56.42       345.96       135.91       182.01        55.59 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       19.56        21.67        28.80        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF 
       16.96       144.76       248.61       122.73         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC 
       23.47       138.77        48.59       228.59         7.76       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
       53.52        15.45        32.71        11.41       148.77       120.46 
TCGA-GN-A265 
       84.72 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              6.41               3.68 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            215.44             357.37 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             61.18              53.52 
[1] "6.4 - 215.4 (61.2)" "3.7 - 357.4 (53.5)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D18V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12P GAIN MUTATED                    1             0
  12P GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12P GAIN MUTATED                                                                                          3
  12P GAIN WILD-TYPE                                                                                        9
                    vv
clus                 REGIONAL LYMPH NODE
  12P GAIN MUTATED                     7
  12P GAIN WILD-TYPE                  41
D18V3, multiclass
                                                                                          clus
vv                                                                                         12P GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         12P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  9
  REGIONAL LYMPH NODE                                                                                      41
D18V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   10
  12P GAIN WILD-TYPE   21   35
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                1                 21
  MALE                 10                 35
                    vv
clus                 M0 M1 M1A M1B M1C
  12P GAIN MUTATED   10  1   0   0   0
  12P GAIN WILD-TYPE 46  0   1   1   2
D18V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  12P GAIN MUTATED    3  0   1   2   1   1   1  2  0
  12P GAIN WILD-TYPE 30  1   1   5   0   4   2  5  2
D18V6, multiclass
D18V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12P GAIN MUTATED             0       2        1        0        0         0
  12P GAIN WILD-TYPE           2       8        1        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  12P GAIN MUTATED           0         3          1          2          1
  12P GAIN WILD-TYPE         2         2          1          5          8
                    vv
clus                 STAGE IV
  12P GAIN MUTATED          1
  12P GAIN WILD-TYPE        2
D18V8, multiclass

Clustering(19) Variable = 12q gain mutation analysis
D19V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    3  2
  12Q GAIN WILD-TYPE 29 32
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                 61 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 32 
$`12Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-DA-A3F5 TCGA-EE-A2A6 TCGA-EE-A2GB 
       71.80        31.59       215.44        58.75        47.54 

$`12Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
      112.54       121.22        23.77        11.87        12.10        58.03 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY 
       60.23         9.30       148.31         6.38        36.03       117.17 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       15.68        26.86       109.64        78.87       168.26        63.32 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
       47.84        39.62        32.19        44.35        56.42       345.96 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
      135.91       182.01        55.59        19.56        21.67       129.24 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.80        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      248.61       122.73         3.68        13.81        23.47       138.77 
TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
        6.41        48.59       228.59         7.76       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
       15.45        32.71       101.26        11.41       148.77       120.46 
TCGA-GN-A265 
       84.72 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             31.59               3.68 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            215.44             357.37 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             58.75              55.59 
[1] "31.6 - 215.4 (58.8)" "3.7 - 357.4 (55.6)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D19V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12Q GAIN MUTATED                    0             0
  12Q GAIN WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12Q GAIN MUTATED                                                                                          1
  12Q GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  12Q GAIN MUTATED                     4
  12Q GAIN WILD-TYPE                  44
D19V3, multiclass
                                                                                          clus
vv                                                                                         12Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         12Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      44
D19V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0    5
  12Q GAIN WILD-TYPE   22   40
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                0                 22
  MALE                  5                 40
                    vv
clus                 M0 M1 M1A M1B M1C
  12Q GAIN MUTATED    5  0   0   0   0
  12Q GAIN WILD-TYPE 51  1   1   1   2
D19V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  12Q GAIN MUTATED    1  0   1   1   1   0   0  1  0
  12Q GAIN WILD-TYPE 32  1   1   6   0   5   3  6  2
D19V6, multiclass
D19V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12Q GAIN MUTATED             0       0        1        0        0         0
  12Q GAIN WILD-TYPE           2      10        1        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  12Q GAIN MUTATED           0         1          1          1          1
  12Q GAIN WILD-TYPE         2         4          1          6          8
                    vv
clus                 STAGE IV
  12Q GAIN MUTATED          0
  12Q GAIN WILD-TYPE        3
D19V8, multiclass

Clustering(20) Variable = 13q gain mutation analysis
D20V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    3  5
  13Q GAIN WILD-TYPE 29 29
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                 58 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 29 
$`13Q GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A1I7 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29P TCGA-EE-A2GB 
       60.23        61.18       168.26        63.32        56.42        47.54 
TCGA-EE-A3AF TCGA-FS-A1Z7 
       13.81         7.76 

$`13Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       12.10        58.03         9.30       148.31         6.38        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
      117.17        20.38       176.55        35.93       107.34        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C 
      215.44        15.68        26.86       109.64        78.87        47.84 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GE 
       39.62        32.19        44.35       345.96        58.75       135.91 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
      182.01        55.59        19.56        21.67       129.24        28.80 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP 
       19.76       103.27       103.17        16.96       144.76       248.61 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX 
      122.73         3.68        23.47       138.77         6.41        48.59 
TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM 
      228.59       357.37        53.52        15.45        32.71       101.26 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       11.41       148.77       120.46        84.72 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              7.76               3.68 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            168.26             357.37 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            58.325             54.755 
[1] "7.8 - 168.3 (58.3)" "3.7 - 357.4 (54.8)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D20V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  13Q GAIN MUTATED                    2             0
  13Q GAIN WILD-TYPE                  4             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  13Q GAIN MUTATED                                                                                          1
  13Q GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  13Q GAIN MUTATED                     5
  13Q GAIN WILD-TYPE                  43
D20V3, multiclass
                                                                                          clus
vv                                                                                         13Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         13Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        4
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      43
D20V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    5
  13Q GAIN WILD-TYPE   19   40
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                3                 19
  MALE                  5                 40
                    vv
clus                 M0 M1 M1A M1B M1C
  13Q GAIN MUTATED    7  0   0   0   0
  13Q GAIN WILD-TYPE 49  1   1   1   2
D20V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  13Q GAIN MUTATED    2  0   2   2   0   1   0  0  0
  13Q GAIN WILD-TYPE 31  1   0   5   1   4   3  7  2
D20V6, multiclass
D20V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  13Q GAIN MUTATED             0       1        0        0        0         0
  13Q GAIN WILD-TYPE           2       9        2        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  13Q GAIN MUTATED           1         1          2          1          1
  13Q GAIN WILD-TYPE         1         4          0          6          8
                    vv
clus                 STAGE IV
  13Q GAIN MUTATED          0
  13Q GAIN WILD-TYPE        3
D20V8, multiclass

Clustering(21) Variable = 14q gain mutation analysis
D21V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED    2  3
  14Q GAIN WILD-TYPE 30 31
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 5                 61 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                 31 
$`14Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-EE-A20H TCGA-EE-A2GH 
       31.59       176.55        61.18       168.26       182.01 

$`14Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
      112.54        71.80       121.22        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       58.03        60.23         9.30       148.31         6.38        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 
      117.17        20.38        35.93       107.34        53.92       215.44 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C 
       15.68        26.86       109.64        78.87        63.32        47.84 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       39.62        32.19        44.35        56.42       345.96        58.75 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
       47.54       135.91        55.59        19.56        21.67       129.24 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.80        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      248.61       122.73         3.68        13.81        23.47       138.77 
TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
        6.41        48.59       228.59         7.76       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
       15.45        32.71       101.26        11.41       148.77       120.46 
TCGA-GN-A265 
       84.72 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             31.59               3.68 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            182.01             357.37 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            168.26              53.92 
[1] "31.6 - 182.0 (168.3)" "3.7 - 357.4 (53.9)"  
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D21V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  14Q GAIN MUTATED                    1             0
  14Q GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  14Q GAIN MUTATED                                                                                          1
  14Q GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  14Q GAIN MUTATED                     3
  14Q GAIN WILD-TYPE                  45
D21V3, multiclass
                                                                                          clus
vv                                                                                         14Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         14Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      45
D21V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    5
  14Q GAIN WILD-TYPE   22   40
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                0                 22
  MALE                  5                 40
                    vv
clus                 M0 M1 M1A M1B M1C
  14Q GAIN MUTATED    5  0   0   0   0
  14Q GAIN WILD-TYPE 51  1   1   1   2
D21V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  14Q GAIN MUTATED    2  0   0   0   1   2   0  0  0
  14Q GAIN WILD-TYPE 31  1   2   7   0   3   3  7  2
D21V6, multiclass
D21V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  14Q GAIN MUTATED             0       2        0        0        0         0
  14Q GAIN WILD-TYPE           2       8        2        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  14Q GAIN MUTATED           0         0          0          2          1
  14Q GAIN WILD-TYPE         2         5          2          5          8
                    vv
clus                 STAGE IV
  14Q GAIN MUTATED          0
  14Q GAIN WILD-TYPE        3
D21V8, multiclass

Clustering(22) Variable = 15q gain mutation analysis
D22V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    3  8
  15Q GAIN WILD-TYPE 29 26
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                 55 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 8                 26 
$`15Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A3CE TCGA-DA-A1HW TCGA-DA-A1I7 
      112.54        31.59        23.77        60.23        36.03        61.18 
TCGA-DA-A3F5 TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A2M6 TCGA-FS-A1ZD 
      215.44        26.86       168.26       129.24        53.52 

$`15Q GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO 
       71.80       121.22        11.87        12.10        58.03         9.30 
TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
      148.31         6.38       117.17        20.38       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A 
      107.34        53.92        15.68       109.64        78.87        63.32 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
       47.84        39.62        32.19        44.35        56.42       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT 
       58.75        47.54       135.91       182.01        55.59        19.56 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       21.67        28.80        19.76       103.27       103.17        16.96 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      144.76       248.61       122.73         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC 
      138.77         6.41        48.59       228.59         7.76       357.37 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
       15.45        32.71       101.26        11.41       148.77       120.46 
TCGA-GN-A265 
       84.72 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             23.77               3.68 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            215.44             357.37 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             60.23              55.59 
[1] "23.8 - 215.4 (60.2)" "3.7 - 357.4 (55.6)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "15Q GAIN MUTATED"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "15Q GAIN MUTATED"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "15Q GAIN MUTATED"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D22V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  15Q GAIN MUTATED                    1             0
  15Q GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  15Q GAIN MUTATED                                                                                          1
  15Q GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  15Q GAIN MUTATED                     9
  15Q GAIN WILD-TYPE                  39
D22V3, multiclass
                                                                                          clus
vv                                                                                         15Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     9
                                                                                          clus
vv                                                                                         15Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      39
D22V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2    9
  15Q GAIN WILD-TYPE   20   36
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                2                 20
  MALE                  9                 36
                    vv
clus                 M0 M1 M1A M1B M1C
  15Q GAIN MUTATED   11  0   0   0   0
  15Q GAIN WILD-TYPE 45  1   1   1   2
D22V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  15Q GAIN MUTATED    5  0   0   2   1   1   0  2  0
  15Q GAIN WILD-TYPE 28  1   2   5   0   4   3  5  2
D22V6, multiclass
D22V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  15Q GAIN MUTATED             1       3        0        0        0         1
  15Q GAIN WILD-TYPE           1       7        2        5        8         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  15Q GAIN MUTATED           0         1          0          3          2
  15Q GAIN WILD-TYPE         2         4          2          4          7
                    vv
clus                 STAGE IV
  15Q GAIN MUTATED          0
  15Q GAIN WILD-TYPE        3
D22V8, multiclass

Clustering(23) Variable = 16p gain mutation analysis
D23V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    2  3
  16P GAIN WILD-TYPE 30 31
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 61 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 31 
$`16P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3CE TCGA-EE-A20H TCGA-EE-A2GB TCGA-EE-A2M6 
       71.80        60.23       168.26        47.54       129.24 

$`16P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
      112.54       121.22        31.59        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY 
       58.03         9.30       148.31         6.38        36.03       117.17 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A 
      215.44        15.68        26.86       109.64        78.87        63.32 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
       47.84        39.62        32.19        44.35        56.42       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       58.75       135.91       182.01        55.59        19.56        21.67 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.80        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      248.61       122.73         3.68        13.81        23.47       138.77 
TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
        6.41        48.59       228.59         7.76       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
       15.45        32.71       101.26        11.41       148.77       120.46 
TCGA-GN-A265 
       84.72 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             47.54               3.68 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            168.26             357.37 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             71.80              53.92 
[1] "47.5 - 168.3 (71.8)" "3.7 - 357.4 (53.9)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D23V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16P GAIN MUTATED                    1             0
  16P GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16P GAIN MUTATED                                                                                          1
  16P GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  16P GAIN MUTATED                     3
  16P GAIN WILD-TYPE                  45
D23V3, multiclass
                                                                                          clus
vv                                                                                         16P GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         16P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      45
D23V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1    4
  16P GAIN WILD-TYPE   21   41
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                1                 21
  MALE                  4                 41
                    vv
clus                 M0 M1 M1A M1B M1C
  16P GAIN MUTATED    5  0   0   0   0
  16P GAIN WILD-TYPE 51  1   1   1   2
D23V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  16P GAIN MUTATED    2  0   1   2   0   0   0  0  0
  16P GAIN WILD-TYPE 31  1   1   5   1   5   3  7  2
D23V6, multiclass
D23V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16P GAIN MUTATED             0       2        0        0        0         0
  16P GAIN WILD-TYPE           2       8        2        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  16P GAIN MUTATED           0         2          1          0          0
  16P GAIN WILD-TYPE         2         3          1          7          9
                    vv
clus                 STAGE IV
  16P GAIN MUTATED          0
  16P GAIN WILD-TYPE        3
D23V8, multiclass

Clustering(24) Variable = 16q gain mutation analysis
D24V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    2  3
  16Q GAIN WILD-TYPE 30 31
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                 61 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 31 
$`16Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3CE TCGA-EE-A20H TCGA-EE-A2GB TCGA-EE-A2M6 
       71.80        60.23       168.26        47.54       129.24 

$`16Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
      112.54       121.22        31.59        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY 
       58.03         9.30       148.31         6.38        36.03       117.17 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A 
      215.44        15.68        26.86       109.64        78.87        63.32 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
       47.84        39.62        32.19        44.35        56.42       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       58.75       135.91       182.01        55.59        19.56        21.67 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.80        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      248.61       122.73         3.68        13.81        23.47       138.77 
TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
        6.41        48.59       228.59         7.76       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
       15.45        32.71       101.26        11.41       148.77       120.46 
TCGA-GN-A265 
       84.72 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             47.54               3.68 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            168.26             357.37 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             71.80              53.92 
[1] "47.5 - 168.3 (71.8)" "3.7 - 357.4 (53.9)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D24V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16Q GAIN MUTATED                    1             0
  16Q GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16Q GAIN MUTATED                                                                                          1
  16Q GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  16Q GAIN MUTATED                     4
  16Q GAIN WILD-TYPE                  44
D24V3, multiclass
                                                                                          clus
vv                                                                                         16Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         16Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      44
D24V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    5
  16Q GAIN WILD-TYPE   21   40
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                1                 21
  MALE                  5                 40
                    vv
clus                 M0 M1 M1A M1B M1C
  16Q GAIN MUTATED    6  0   0   0   0
  16Q GAIN WILD-TYPE 50  1   1   1   2
D24V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  16Q GAIN MUTATED    2  0   1   3   0   0   0  0  0
  16Q GAIN WILD-TYPE 31  1   1   4   1   5   3  7  2
D24V6, multiclass
D24V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16Q GAIN MUTATED             0       2        0        0        0         0
  16Q GAIN WILD-TYPE           2       8        2        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  16Q GAIN MUTATED           0         2          1          1          0
  16Q GAIN WILD-TYPE         2         3          1          6          9
                    vv
clus                 STAGE IV
  16Q GAIN MUTATED          0
  16Q GAIN WILD-TYPE        3
D24V8, multiclass

Clustering(25) Variable = 17p gain mutation analysis
D25V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    5  2
  17P GAIN WILD-TYPE 27 32
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 7                 59 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 32 
$`17P GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A1I7 TCGA-EE-A20F TCGA-EE-A29P TCGA-EE-A2A6 TCGA-EE-A3AG 
       60.23        61.18        78.87        56.42        58.75        23.47 
TCGA-FS-A1ZD 
       53.52 

$`17P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       12.10        58.03         9.30       148.31         6.38        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
      117.17        20.38       176.55        35.93       107.34        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
      215.44        15.68        26.86       109.64       168.26        63.32 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2GB 
       47.84        39.62        32.19        44.35       345.96        47.54 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
      135.91       182.01        55.59        19.56        21.67       129.24 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.80        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-ER-A19J 
      248.61       122.73         3.68        13.81       138.77         6.41 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH 
       48.59       228.59         7.76       357.37        15.45        32.71 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
      101.26        11.41       148.77       120.46        84.72 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             23.47               3.68 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             78.87             357.37 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             58.75              53.92 
[1] "23.5 - 78.9 (58.8)" "3.7 - 357.4 (53.9)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D25V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17P GAIN MUTATED                    0             0
  17P GAIN WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17P GAIN MUTATED                                                                                          2
  17P GAIN WILD-TYPE                                                                                       10
                    vv
clus                 REGIONAL LYMPH NODE
  17P GAIN MUTATED                     5
  17P GAIN WILD-TYPE                  43
D25V3, multiclass
                                                                                          clus
vv                                                                                         17P GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         17P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 10
  REGIONAL LYMPH NODE                                                                                      43
D25V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2    5
  17P GAIN WILD-TYPE   20   40
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                2                 20
  MALE                  5                 40
                    vv
clus                 M0 M1 M1A M1B M1C
  17P GAIN MUTATED    6  0   0   0   0
  17P GAIN WILD-TYPE 50  1   1   1   2
D25V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  17P GAIN MUTATED    4  0   0   1   0   1   0  0  0
  17P GAIN WILD-TYPE 29  1   2   6   1   4   3  7  2
D25V6, multiclass
D25V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17P GAIN MUTATED             0       0        1        0        1         1
  17P GAIN WILD-TYPE           2      10        1        5        7         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  17P GAIN MUTATED           1         1          0          1          0
  17P GAIN WILD-TYPE         1         4          2          6          9
                    vv
clus                 STAGE IV
  17P GAIN MUTATED          0
  17P GAIN WILD-TYPE        3
D25V8, multiclass

Clustering(26) Variable = 17q gain mutation analysis
D26V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    4  2
  17Q GAIN WILD-TYPE 28 32
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 6                 60 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 32 
$`17Q GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A1I7 TCGA-EE-A20F TCGA-EE-A29P TCGA-EE-A2A6 TCGA-FS-A1ZD 
       60.23        61.18        78.87        56.42        58.75        53.52 

$`17Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       12.10        58.03         9.30       148.31         6.38        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
      117.17        20.38       176.55        35.93       107.34        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
      215.44        15.68        26.86       109.64       168.26        63.32 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2GB 
       47.84        39.62        32.19        44.35       345.96        47.54 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
      135.91       182.01        55.59        19.56        21.67       129.24 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.80        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      248.61       122.73         3.68        13.81        23.47       138.77 
TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZF 
        6.41        48.59       228.59         7.76       357.37        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       32.71       101.26        11.41       148.77       120.46        84.72 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             53.52               3.68 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             78.87             357.37 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            59.490             51.255 
[1] "53.5 - 78.9 (59.5)" "3.7 - 357.4 (51.3)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D26V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17Q GAIN MUTATED                    0             0
  17Q GAIN WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17Q GAIN MUTATED                                                                                          1
  17Q GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  17Q GAIN MUTATED                     5
  17Q GAIN WILD-TYPE                  43
D26V3, multiclass
                                                                                          clus
vv                                                                                         17Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         17Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      43
D26V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2    4
  17Q GAIN WILD-TYPE   20   41
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                2                 20
  MALE                  4                 41
                    vv
clus                 M0 M1 M1A M1B M1C
  17Q GAIN MUTATED    6  0   0   0   0
  17Q GAIN WILD-TYPE 50  1   1   1   2
D26V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  17Q GAIN MUTATED    4  0   0   1   0   1   0  0  0
  17Q GAIN WILD-TYPE 29  1   2   6   1   4   3  7  2
D26V6, multiclass
D26V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17Q GAIN MUTATED             0       0        1        0        1         1
  17Q GAIN WILD-TYPE           2      10        1        5        7         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  17Q GAIN MUTATED           1         1          0          1          0
  17Q GAIN WILD-TYPE         1         4          2          6          9
                    vv
clus                 STAGE IV
  17Q GAIN MUTATED          0
  17Q GAIN WILD-TYPE        3
D26V8, multiclass

Clustering(27) Variable = 18p gain mutation analysis
D27V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    5  5
  18P GAIN WILD-TYPE 27 29
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                10                 56 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                 29 
$`18P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-DA-A1I0 TCGA-EE-A29E TCGA-EE-A2GB 
      112.54        31.59        60.23        20.38        39.62        47.54 
TCGA-EE-A2GH TCGA-EE-A2MP TCGA-EE-A3AD TCGA-FS-A1ZC 
      182.01       248.61         3.68       357.37 

$`18P GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       71.80       121.22        23.77        11.87        12.10        58.03 
TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        9.30       148.31         6.38        36.03       117.17       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
       35.93       107.34        61.18        53.92       215.44        15.68 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       26.86       109.64        78.87       168.26        63.32        47.84 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GE 
       32.19        44.35        56.42       345.96        58.75       135.91 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.59        19.56        21.67       129.24        28.80        19.76 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A3AB TCGA-EE-A3AF 
      103.27       103.17        16.96       144.76       122.73        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
       23.47       138.77         6.41        48.59       228.59         7.76 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
       53.52        15.45        32.71       101.26        11.41       148.77 
TCGA-GN-A262 TCGA-GN-A265 
      120.46        84.72 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              3.68               6.38 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            357.37             345.96 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            53.885             56.005 
[1] "3.7 - 357.4 (53.9)" "6.4 - 346.0 (56.0)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D27V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18P GAIN MUTATED                    1             0
  18P GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18P GAIN MUTATED                                                                                          1
  18P GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  18P GAIN MUTATED                     8
  18P GAIN WILD-TYPE                  40
D27V3, multiclass
                                                                                          clus
vv                                                                                         18P GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     8
                                                                                          clus
vv                                                                                         18P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      40
D27V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    8
  18P GAIN WILD-TYPE   20   37
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                2                 20
  MALE                  8                 37
                    vv
clus                 M0 M1 M1A M1B M1C
  18P GAIN MUTATED    8  0   1   0   0
  18P GAIN WILD-TYPE 48  1   0   1   2
D27V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  18P GAIN MUTATED    4  0   1   2   1   0   0  1  0
  18P GAIN WILD-TYPE 29  1   1   5   0   5   3  6  2
D27V6, multiclass
D27V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18P GAIN MUTATED             2       2        0        0        0         0
  18P GAIN WILD-TYPE           0       8        2        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  18P GAIN MUTATED           0         1          1          2          1
  18P GAIN WILD-TYPE         2         4          1          5          8
                    vv
clus                 STAGE IV
  18P GAIN MUTATED          0
  18P GAIN WILD-TYPE        3
D27V8, multiclass

Clustering(28) Variable = 18q gain mutation analysis
D28V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    2  2
  18Q GAIN WILD-TYPE 30 32
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 62 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 32 
$`18Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-EE-A2GH TCGA-EE-A3AD TCGA-FS-A1ZC 
      112.54       182.01         3.68       357.37 

$`18Q GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       71.80       121.22        31.59        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       58.03        60.23         9.30       148.31         6.38        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.17        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       53.92       215.44        15.68        26.86       109.64        78.87 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
      168.26        63.32        47.84        39.62        32.19        44.35 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GS 
       56.42       345.96        58.75        47.54       135.91        55.59 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME 
       19.56        21.67       129.24        28.80        19.76       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AF 
      103.17        16.96       144.76       248.61       122.73        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
       23.47       138.77         6.41        48.59       228.59         7.76 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
       53.52        15.45        32.71       101.26        11.41       148.77 
TCGA-GN-A262 TCGA-GN-A265 
      120.46        84.72 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              3.68               6.38 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            357.37             345.96 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
           147.275             54.755 
[1] "3.7 - 357.4 (147.3)" "6.4 - 346.0 (54.8)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
[1] "hr=" "3.5"
D28V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18Q GAIN MUTATED                    1             0
  18Q GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18Q GAIN MUTATED                                                                                          0
  18Q GAIN WILD-TYPE                                                                                       12
                    vv
clus                 REGIONAL LYMPH NODE
  18Q GAIN MUTATED                     3
  18Q GAIN WILD-TYPE                  45
D28V3, multiclass
                                                                                          clus
vv                                                                                         18Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         18Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 12
  REGIONAL LYMPH NODE                                                                                      45
D28V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    4
  18Q GAIN WILD-TYPE   22   41
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                0                 22
  MALE                  4                 41
                    vv
clus                 M0 M1 M1A M1B M1C
  18Q GAIN MUTATED    3  0   0   0   0
  18Q GAIN WILD-TYPE 53  1   1   1   2
D28V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  18Q GAIN MUTATED    3  0   0   0   0   0   0  0  0
  18Q GAIN WILD-TYPE 30  1   2   7   1   5   3  7  2
D28V6, multiclass
D28V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18Q GAIN MUTATED             2       1        0        0        0         0
  18Q GAIN WILD-TYPE           0       9        2        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  18Q GAIN MUTATED           0         0          0          0          0
  18Q GAIN WILD-TYPE         2         5          2          7          9
                    vv
clus                 STAGE IV
  18Q GAIN MUTATED          0
  18Q GAIN WILD-TYPE        3
D28V8, multiclass

Clustering(29) Variable = 19p gain mutation analysis
D29V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    2  4
  19P GAIN WILD-TYPE 30 30
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                 60 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                 30 
$`19P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-DA-A1I0 TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      112.54        20.38        55.59       129.24       357.37        53.52 

$`19P GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       71.80       121.22        31.59        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       58.03        60.23         9.30       148.31         6.38        36.03 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      117.17       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
      215.44        15.68        26.86       109.64        78.87       168.26 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       63.32        47.84        39.62        32.19        44.35        56.42 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GT 
      345.96        58.75        47.54       135.91       182.01        19.56 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       21.67        28.80        19.76       103.27       103.17        16.96 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      144.76       248.61       122.73         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZF 
      138.77         6.41        48.59       228.59         7.76        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       32.71       101.26        11.41       148.77       120.46        84.72 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             20.38               3.68 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            357.37             345.96 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            84.065             55.170 
[1] "20.4 - 357.4 (84.1)" "3.7 - 346.0 (55.2)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D29V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19P GAIN MUTATED                    1             0
  19P GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19P GAIN MUTATED                                                                                          1
  19P GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  19P GAIN MUTATED                     4
  19P GAIN WILD-TYPE                  44
D29V3, multiclass
                                                                                          clus
vv                                                                                         19P GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         19P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      44
D29V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    5
  19P GAIN WILD-TYPE   21   40
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                1                 21
  MALE                  5                 40
                    vv
clus                 M0 M1 M1A M1B M1C
  19P GAIN MUTATED    5  0   1   0   0
  19P GAIN WILD-TYPE 51  1   0   1   2
D29V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  19P GAIN MUTATED    5  0   0   0   0   0   0  1  0
  19P GAIN WILD-TYPE 28  1   2   7   1   5   3  6  2
D29V6, multiclass
D29V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19P GAIN MUTATED             2       1        0        1        0         1
  19P GAIN WILD-TYPE           0       9        2        4        8         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  19P GAIN MUTATED           0         0          0          0          1
  19P GAIN WILD-TYPE         2         5          2          7          8
                    vv
clus                 STAGE IV
  19P GAIN MUTATED          0
  19P GAIN WILD-TYPE        3
D29V8, multiclass

Clustering(30) Variable = 19q gain mutation analysis
D30V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    3  4
  19Q GAIN WILD-TYPE 29 30
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                 59 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                 30 
$`19Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3CE TCGA-EE-A29T TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-FS-A1ZC 
      112.54        60.23       345.96        55.59       129.24       357.37 
TCGA-FS-A1ZD 
       53.52 

$`19Q GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       71.80       121.22        31.59        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY 
       58.03         9.30       148.31         6.38        36.03       117.17 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
      215.44        15.68        26.86       109.64        78.87       168.26 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       63.32        47.84        39.62        32.19        44.35        56.42 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GT TCGA-EE-A2M5 
       58.75        47.54       135.91       182.01        19.56        21.67 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.80        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      248.61       122.73         3.68        13.81        23.47       138.77 
TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZF TCGA-FS-A1ZH 
        6.41        48.59       228.59         7.76        15.45        32.71 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
      101.26        11.41       148.77       120.46        84.72 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             53.52               3.68 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            357.37             248.61 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            112.54              48.59 
[1] "53.5 - 357.4 (112.5)" "3.7 - 248.6 (48.6)"  
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "hr=" "2"  
D30V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19Q GAIN MUTATED                    1             0
  19Q GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19Q GAIN MUTATED                                                                                          0
  19Q GAIN WILD-TYPE                                                                                       12
                    vv
clus                 REGIONAL LYMPH NODE
  19Q GAIN MUTATED                     6
  19Q GAIN WILD-TYPE                  42
D30V3, multiclass
                                                                                          clus
vv                                                                                         19Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     6
                                                                                          clus
vv                                                                                         19Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 12
  REGIONAL LYMPH NODE                                                                                      42
D30V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3    4
  19Q GAIN WILD-TYPE   19   41
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                3                 19
  MALE                  4                 41
                    vv
clus                 M0 M1 M1A M1B M1C
  19Q GAIN MUTATED    7  0   0   0   0
  19Q GAIN WILD-TYPE 49  1   1   1   2
D30V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  19Q GAIN MUTATED    5  0   0   1   0   0   0  0  1
  19Q GAIN WILD-TYPE 28  1   2   6   1   5   3  7  1
D30V6, multiclass
D30V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19Q GAIN MUTATED             2       1        0        1        0         1
  19Q GAIN WILD-TYPE           0       9        2        4        8         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  19Q GAIN MUTATED           0         1          0          0          0
  19Q GAIN WILD-TYPE         2         4          2          7          9
                    vv
clus                 STAGE IV
  19Q GAIN MUTATED          0
  19Q GAIN WILD-TYPE        3
D30V8, multiclass

Clustering(31) Variable = 20p gain mutation analysis
D31V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   11 13
  20P GAIN WILD-TYPE 21 21
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                24                 42 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                13                 21 
$`20P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-D9-A1JX TCGA-DA-A1I0 TCGA-DA-A1I2 
      112.54        31.59        60.23         6.38        20.38       176.55 
TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A2A6 
       61.18       215.44       109.64       168.26        63.32        58.75 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MH TCGA-EE-A2MP 
       47.54       182.01        21.67       129.24        16.96       248.61 
TCGA-ER-A19J TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS 
        6.41         7.76       357.37        53.52       101.26       148.77 

$`20P GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       71.80       121.22        23.77        11.87        12.10        58.03 
TCGA-D3-A3MO TCGA-D9-A148 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 
        9.30       148.31        36.03       117.17        35.93       107.34 
TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E 
       53.92        15.68        26.86        78.87        47.84        39.62 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2GE TCGA-EE-A2GS 
       32.19        44.35        56.42       345.96       135.91        55.59 
TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MK 
       19.56        28.80        19.76       103.27       103.17       144.76 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-FS-A1YX 
      122.73         3.68        13.81        23.47       138.77        48.59 
TCGA-FS-A1YY TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
      228.59        15.45        32.71        11.41       120.46        84.72 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              6.38               3.68 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            357.37             345.96 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            62.250             48.215 
[1] "6.4 - 357.4 (62.2)" "3.7 - 346.0 (48.2)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D31V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20P GAIN MUTATED                    3             0
  20P GAIN WILD-TYPE                  3             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20P GAIN MUTATED                                                                                          4
  20P GAIN WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  20P GAIN MUTATED                    17
  20P GAIN WILD-TYPE                  31
D31V3, multiclass
                                                                                          clus
vv                                                                                         20P GAIN MUTATED
  DISTANT METASTASIS                                                                                      3
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                    17
                                                                                          clus
vv                                                                                         20P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        3
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      31
D31V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4   20
  20P GAIN WILD-TYPE   18   25
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                4                 18
  MALE                 20                 25
                    vv
clus                 M0 M1 M1A M1B M1C
  20P GAIN MUTATED   22  1   1   0   0
  20P GAIN WILD-TYPE 34  0   0   1   2
D31V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  20P GAIN MUTATED   12  0   2   2   1   2   1  3  1
  20P GAIN WILD-TYPE 21  1   0   5   0   3   2  4  1
D31V6, multiclass
D31V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  20P GAIN MUTATED             2       5        1        0        3         1
  20P GAIN WILD-TYPE           0       5        1        5        5         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  20P GAIN MUTATED           0         2          2          2          4
  20P GAIN WILD-TYPE         2         3          0          5          5
                    vv
clus                 STAGE IV
  20P GAIN MUTATED          1
  20P GAIN WILD-TYPE        2
D31V8, multiclass

Clustering(32) Variable = 20q gain mutation analysis
D32V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   15 13
  20Q GAIN WILD-TYPE 17 21
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                28                 38 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                13                 21 
$`20Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1I0 
      112.54        31.59        60.23       148.31         6.38        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
      176.55        61.18       215.44       109.64       168.26        63.32 
TCGA-EE-A29E TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2M6 
       39.62        58.75        47.54       182.01        21.67       129.24 
TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AG TCGA-ER-A19J TCGA-FS-A1Z7 
       16.96       248.61         3.68        23.47         6.41         7.76 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS 
      357.37        53.52       101.26       148.77 

$`20Q GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       71.80       121.22        23.77        11.87        12.10        58.03 
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
        9.30        36.03       117.17        35.93       107.34        53.92 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
       15.68        26.86        78.87        47.84        32.19        44.35 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2GE TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M7 
       56.42       345.96       135.91        55.59        19.56        28.80 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A3AB TCGA-EE-A3AF 
       19.76       103.27       103.17       144.76       122.73        13.81 
TCGA-EE-A3AH TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZR 
      138.77        48.59       228.59        15.45        32.71        11.41 
TCGA-GN-A262 TCGA-GN-A265 
      120.46        84.72 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              3.68               9.30 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            357.37             345.96 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            60.705             51.255 
[1] "3.7 - 357.4 (60.7)" "9.3 - 346.0 (51.3)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D32V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20Q GAIN MUTATED                    3             0
  20Q GAIN WILD-TYPE                  3             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20Q GAIN MUTATED                                                                                          5
  20Q GAIN WILD-TYPE                                                                                        7
                    vv
clus                 REGIONAL LYMPH NODE
  20Q GAIN MUTATED                    20
  20Q GAIN WILD-TYPE                  28
D32V3, multiclass
                                                                                          clus
vv                                                                                         20Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      3
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    20
                                                                                          clus
vv                                                                                         20Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        3
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  7
  REGIONAL LYMPH NODE                                                                                      28
D32V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4   24
  20Q GAIN WILD-TYPE   18   21
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                4                 18
  MALE                 24                 21
                    vv
clus                 M0 M1 M1A M1B M1C
  20Q GAIN MUTATED   23  1   1   1   0
  20Q GAIN WILD-TYPE 33  0   0   0   2
D32V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  20Q GAIN MUTATED   12  0   2   3   1   2   1  4  1
  20Q GAIN WILD-TYPE 21  1   0   4   0   3   2  3  1
D32V6, multiclass
D32V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  20Q GAIN MUTATED             2       5        1        0        3         1
  20Q GAIN WILD-TYPE           0       5        1        5        5         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  20Q GAIN MUTATED           0         2          2          3          4
  20Q GAIN WILD-TYPE         2         3          0          4          5
                    vv
clus                 STAGE IV
  20Q GAIN MUTATED          1
  20Q GAIN WILD-TYPE        2
D32V8, multiclass

Clustering(33) Variable = 21q gain mutation analysis
D33V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    1  3
  21Q GAIN WILD-TYPE 31 31
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 62 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 31 
$`21Q GAIN MUTATED`
TCGA-EE-A20H TCGA-EE-A29A TCGA-FS-A1ZD TCGA-FS-A1ZS 
      168.26        63.32        53.52       148.77 

$`21Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX 
       12.10        58.03        60.23         9.30       148.31         6.38 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.17        20.38       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
       61.18        53.92       215.44        15.68        26.86       109.64 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       78.87        47.84        39.62        32.19        44.35        56.42 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS 
      345.96        58.75        47.54       135.91       182.01        55.59 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME 
       19.56        21.67       129.24        28.80        19.76       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD 
      103.17        16.96       144.76       248.61       122.73         3.68 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY 
       13.81        23.47       138.77         6.41        48.59       228.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR 
        7.76       357.37        15.45        32.71       101.26        11.41 
TCGA-GN-A262 TCGA-GN-A265 
      120.46        84.72 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             53.52               3.68 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            168.26             357.37 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
           106.045             54.755 
[1] "53.5 - 168.3 (106.0)" "3.7 - 357.4 (54.8)"  
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED"   "21Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED"   "21Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED"   "21Q GAIN MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D33V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  21Q GAIN MUTATED                    2             0
  21Q GAIN WILD-TYPE                  4             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  21Q GAIN MUTATED                                                                                          0
  21Q GAIN WILD-TYPE                                                                                       12
                    vv
clus                 REGIONAL LYMPH NODE
  21Q GAIN MUTATED                     2
  21Q GAIN WILD-TYPE                  46
D33V3, multiclass
                                                                                          clus
vv                                                                                         21Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         21Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        4
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 12
  REGIONAL LYMPH NODE                                                                                      46
D33V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    4
  21Q GAIN WILD-TYPE   22   41
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                0                 22
  MALE                  4                 41
                    vv
clus                 M0 M1 M1A M1B M1C
  21Q GAIN MUTATED    4  0   0   0   0
  21Q GAIN WILD-TYPE 52  1   1   1   2
D33V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  21Q GAIN MUTATED    3  0   1   0   0   0   0  0  0
  21Q GAIN WILD-TYPE 30  1   1   7   1   5   3  7  2
D33V6, multiclass
D33V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  21Q GAIN MUTATED             0       1        0        0        1         1
  21Q GAIN WILD-TYPE           2       9        2        5        7         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  21Q GAIN MUTATED           0         0          1          0          0
  21Q GAIN WILD-TYPE         2         5          1          7          9
                    vv
clus                 STAGE IV
  21Q GAIN MUTATED          0
  21Q GAIN WILD-TYPE        3
D33V8, multiclass

Clustering(34) Variable = 22q gain mutation analysis
D34V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   10  7
  22Q GAIN WILD-TYPE 22 27
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                17                 49 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 7                 27 
$`22Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A3MO TCGA-D9-A148 TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1I8 
       31.59         9.30       148.31        20.38        61.18        53.92 
TCGA-DA-A3F5 TCGA-EE-A20H TCGA-EE-A29M TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M6 
      215.44       168.26        44.35        47.54       182.01       129.24 
TCGA-EE-A3AG TCGA-FS-A1YY TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-GN-A265 
       23.47       228.59        53.52       101.26        84.72 

$`22Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
      112.54        71.80       121.22        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
       58.03        60.23         6.38        36.03       117.17       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       35.93       107.34        15.68        26.86       109.64        78.87 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T 
       63.32        47.84        39.62        32.19        56.42       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M7 
       58.75       135.91        55.59        19.56        21.67        28.80 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP 
       19.76       103.27       103.17        16.96       144.76       248.61 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX 
      122.73         3.68        13.81       138.77         6.41        48.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZR TCGA-FS-A1ZS 
        7.76       357.37        15.45        32.71        11.41       148.77 
TCGA-GN-A262 
      120.46 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              9.30               3.68 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            228.59             357.37 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             61.18              55.59 
[1] "9.3 - 228.6 (61.2)" "3.7 - 357.4 (55.6)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
[1] "hr=" "1.6"
D34V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  22Q GAIN MUTATED                    2             1
  22Q GAIN WILD-TYPE                  4             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  22Q GAIN MUTATED                                                                                          6
  22Q GAIN WILD-TYPE                                                                                        6
                    vv
clus                 REGIONAL LYMPH NODE
  22Q GAIN MUTATED                     8
  22Q GAIN WILD-TYPE                  40
D34V3, multiclass
                                                                                          clus
vv                                                                                         22Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                     8
                                                                                          clus
vv                                                                                         22Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        4
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  6
  REGIONAL LYMPH NODE                                                                                      40
D34V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   14
  22Q GAIN WILD-TYPE   19   31
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                3                 19
  MALE                 14                 31
                    vv
clus                 M0 M1 M1A M1B M1C
  22Q GAIN MUTATED   13  0   1   1   0
  22Q GAIN WILD-TYPE 43  1   0   0   2
D34V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  22Q GAIN MUTATED    6  0   1   0   1   1   2  4  0
  22Q GAIN WILD-TYPE 27  1   1   7   0   4   1  3  2
D34V6, multiclass
D34V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  22Q GAIN MUTATED             0       3        0        1        0         2
  22Q GAIN WILD-TYPE           2       7        2        4        8         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  22Q GAIN MUTATED           0         2          1          2          3
  22Q GAIN WILD-TYPE         2         3          1          5          6
                    vv
clus                 STAGE IV
  22Q GAIN MUTATED          0
  22Q GAIN WILD-TYPE        3
D34V8, multiclass

Clustering(35) Variable = 1p loss mutation analysis
D35V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    3  3
  1P LOSS WILD-TYPE 29 31
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                60 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                31 
$`1P LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A20H TCGA-EE-A2MK 
       31.59       176.55        61.18       215.44       168.26       144.76 

$`1P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
      112.54        71.80       121.22        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       58.03        60.23         9.30       148.31         6.38        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F8 
      117.17        20.38        35.93       107.34        53.92        15.68 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       26.86       109.64        78.87        63.32        47.84        39.62 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB 
       32.19        44.35        56.42       345.96        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
      135.91       182.01        55.59        19.56        21.67       129.24 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MP 
       28.80        19.76       103.27       103.17        16.96       248.61 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J 
      122.73         3.68        13.81        23.47       138.77         6.41 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       48.59       228.59         7.76       357.37        53.52        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       32.71       101.26        11.41       148.77       120.46        84.72 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            31.59              3.68 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           215.44            357.37 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           156.51             53.72 
[1] "31.6 - 215.4 (156.5)" "3.7 - 357.4 (53.7)"  
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D35V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1P LOSS MUTATED                    1             0
  1P LOSS WILD-TYPE                  5             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1P LOSS MUTATED                                                                                          1
  1P LOSS WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  1P LOSS MUTATED                     4
  1P LOSS WILD-TYPE                  44
D35V3, multiclass
                                                                                          clus
vv                                                                                         1P LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         1P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     44
D35V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    5
  1P LOSS WILD-TYPE   21   40
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               1                21
  MALE                 5                40
                   vv
clus                M0 M1 M1A M1B M1C
  1P LOSS MUTATED    6  0   0   0   0
  1P LOSS WILD-TYPE 50  1   1   1   2
D35V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  1P LOSS MUTATED    2  0   0   0   1   2   0  1  0
  1P LOSS WILD-TYPE 31  1   2   7   0   3   3  6  2
D35V6, multiclass
D35V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1P LOSS MUTATED             0       1        0        0        1         0
  1P LOSS WILD-TYPE           2       9        2        5        7         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P LOSS MUTATED           0         0          0          2          2
  1P LOSS WILD-TYPE         2         5          2          5          7
                   vv
clus                STAGE IV
  1P LOSS MUTATED          0
  1P LOSS WILD-TYPE        3
D35V8, multiclass

Clustering(36) Variable = 1q loss mutation analysis
D36V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    1  3
  1Q LOSS WILD-TYPE 31 31
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                62 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3                31 
$`1Q LOSS MUTATED`
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-EE-A20H 
      176.55        61.18        53.92       168.26 

$`1Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX 
       12.10        58.03        60.23         9.30       148.31         6.38 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A3F5 
       36.03       117.17        20.38        35.93       107.34       215.44 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C 
       15.68        26.86       109.64        78.87        63.32        47.84 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       39.62        32.19        44.35        56.42       345.96        58.75 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       47.54       135.91       182.01        55.59        19.56        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
      129.24        28.80        19.76       103.27       103.17        16.96 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      144.76       248.61       122.73         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC 
      138.77         6.41        48.59       228.59         7.76       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
       53.52        15.45        32.71       101.26        11.41       148.77 
TCGA-GN-A262 TCGA-GN-A265 
      120.46        84.72 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            53.92              3.68 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           176.55            357.37 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
          114.720            54.555 
[1] "53.9 - 176.6 (114.7)" "3.7 - 357.4 (54.6)"  
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D36V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1Q LOSS MUTATED                    1             0
  1Q LOSS WILD-TYPE                  5             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1Q LOSS MUTATED                                                                                          2
  1Q LOSS WILD-TYPE                                                                                       10
                   vv
clus                REGIONAL LYMPH NODE
  1Q LOSS MUTATED                     1
  1Q LOSS WILD-TYPE                  47
D36V3, multiclass
                                                                                          clus
vv                                                                                         1Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    1
                                                                                          clus
vv                                                                                         1Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                10
  REGIONAL LYMPH NODE                                                                                     47
D36V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1    3
  1Q LOSS WILD-TYPE   21   42
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               1                21
  MALE                 3                42
                   vv
clus                M0 M1 M1A M1B M1C
  1Q LOSS MUTATED    4  0   0   0   0
  1Q LOSS WILD-TYPE 52  1   1   1   2
D36V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  1Q LOSS MUTATED    1  0   0   0   0   2   0  1  0
  1Q LOSS WILD-TYPE 32  1   2   7   1   3   3  6  2
D36V6, multiclass
D36V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1Q LOSS MUTATED             0       1        0        0        0         0
  1Q LOSS WILD-TYPE           2       9        2        5        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q LOSS MUTATED           0         0          0          1          2
  1Q LOSS WILD-TYPE         2         5          2          6          7
                   vv
clus                STAGE IV
  1Q LOSS MUTATED          0
  1Q LOSS WILD-TYPE        3
D36V8, multiclass

Clustering(37) Variable = 2p loss mutation analysis
D37V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    4  3
  2P LOSS WILD-TYPE 28 31
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7                59 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                31 
$`2P LOSS MUTATED`
TCGA-D3-A3C6 TCGA-DA-A1I2 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A2MK TCGA-EE-A3AD 
       58.03       176.55       109.64        78.87       144.76         3.68 
TCGA-FS-A1YY 
      228.59 

$`2P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       12.10        60.23         9.30       148.31         6.38        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
      117.17        20.38        35.93       107.34        61.18        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
      215.44        15.68        26.86       168.26        63.32        47.84 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       39.62        32.19        44.35        56.42       345.96        58.75 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       47.54       135.91       182.01        55.59        19.56        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
      129.24        28.80        19.76       103.27       103.17        16.96 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J 
      248.61       122.73        13.81        23.47       138.77         6.41 
TCGA-FS-A1YX TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
       48.59         7.76       357.37        53.52        15.45        32.71 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
      101.26        11.41       148.77       120.46        84.72 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             3.68              6.38 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           228.59            357.37 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           109.64             53.52 
[1] "3.7 - 228.6 (109.6)" "6.4 - 357.4 (53.5)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D37V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2P LOSS MUTATED                    1             0
  2P LOSS WILD-TYPE                  5             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2P LOSS MUTATED                                                                                          1
  2P LOSS WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  2P LOSS MUTATED                     5
  2P LOSS WILD-TYPE                  43
D37V3, multiclass
                                                                                          clus
vv                                                                                         2P LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         2P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     43
D37V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4    3
  2P LOSS WILD-TYPE   18   42
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               4                18
  MALE                 3                42
                   vv
clus                M0 M1 M1A M1B M1C
  2P LOSS MUTATED    6  0   0   0   0
  2P LOSS WILD-TYPE 50  1   1   1   2
D37V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  2P LOSS MUTATED    5  0   0   0   0   1   0  0  0
  2P LOSS WILD-TYPE 28  1   2   7   1   4   3  7  2
D37V6, multiclass
D37V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2P LOSS MUTATED             0       0        0        1        3         1
  2P LOSS WILD-TYPE           2      10        2        4        5         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P LOSS MUTATED           0         0          0          0          1
  2P LOSS WILD-TYPE         2         5          2          7          8
                   vv
clus                STAGE IV
  2P LOSS MUTATED          0
  2P LOSS WILD-TYPE        3
D37V8, multiclass

Clustering(38) Variable = 2q loss mutation analysis
D38V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    4  3
  2Q LOSS WILD-TYPE 28 31
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                7                59 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                31 
$`2Q LOSS MUTATED`
TCGA-D3-A3C6 TCGA-D9-A148 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A2MK TCGA-EE-A3AF 
       58.03       148.31       109.64        78.87       144.76        13.81 
TCGA-FS-A1YY 
      228.59 

$`2Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY 
       12.10        60.23         9.30         6.38        36.03       117.17 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
      215.44        15.68        26.86       168.26        63.32        47.84 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       39.62        32.19        44.35        56.42       345.96        58.75 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       47.54       135.91       182.01        55.59        19.56        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
      129.24        28.80        19.76       103.27       103.17        16.96 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J 
      248.61       122.73         3.68        23.47       138.77         6.41 
TCGA-FS-A1YX TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
       48.59         7.76       357.37        53.52        15.45        32.71 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
      101.26        11.41       148.77       120.46        84.72 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            13.81              3.68 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           228.59            357.37 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           109.64             53.52 
[1] "13.8 - 228.6 (109.6)" "3.7 - 357.4 (53.5)"  
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D38V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2Q LOSS MUTATED                    1             0
  2Q LOSS WILD-TYPE                  5             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2Q LOSS MUTATED                                                                                          1
  2Q LOSS WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  2Q LOSS MUTATED                     5
  2Q LOSS WILD-TYPE                  43
D38V3, multiclass
                                                                                          clus
vv                                                                                         2Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         2Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     43
D38V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    2
  2Q LOSS WILD-TYPE   17   43
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               5                17
  MALE                 2                43
                   vv
clus                M0 M1 M1A M1B M1C
  2Q LOSS MUTATED    5  0   0   1   0
  2Q LOSS WILD-TYPE 51  1   1   0   2
D38V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  2Q LOSS MUTATED    5  0   0   0   0   0   0  1  0
  2Q LOSS WILD-TYPE 28  1   2   7   1   5   3  6  2
D38V6, multiclass
D38V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2Q LOSS MUTATED             0       0        0        1        3         1
  2Q LOSS WILD-TYPE           2      10        2        4        5         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q LOSS MUTATED           0         0          0          0          0
  2Q LOSS WILD-TYPE         2         5          2          7          9
                   vv
clus                STAGE IV
  2Q LOSS MUTATED          0
  2Q LOSS WILD-TYPE        3
D38V8, multiclass

Clustering(39) Variable = 3p loss mutation analysis
D39V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    4  5
  3P LOSS WILD-TYPE 28 29
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                57 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                29 
$`3P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3C6 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-EE-A3AG 
      112.54        58.03        36.03       176.55        61.18        23.47 
TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-GN-A262 
       48.59       101.26       120.46 

$`3P LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       71.80       121.22        31.59        23.77        11.87        12.10 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I0 
       60.23         9.30       148.31         6.38       117.17        20.38 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 
       35.93       107.34        53.92       215.44        15.68        26.86 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
      109.64        78.87       168.26        63.32        47.84        39.62 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB 
       32.19        44.35        56.42       345.96        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
      135.91       182.01        55.59        19.56        21.67       129.24 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.80        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-ER-A19J 
      248.61       122.73         3.68        13.81       138.77         6.41 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
      228.59         7.76       357.37        53.52        15.45        32.71 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A265 
       11.41       148.77        84.72 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            23.47              3.68 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           176.55            357.37 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            61.18             53.92 
[1] "23.5 - 176.6 (61.2)" "3.7 - 357.4 (53.9)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D39V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3P LOSS MUTATED                    0             0
  3P LOSS WILD-TYPE                  6             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3P LOSS MUTATED                                                                                          5
  3P LOSS WILD-TYPE                                                                                        7
                   vv
clus                REGIONAL LYMPH NODE
  3P LOSS MUTATED                     4
  3P LOSS WILD-TYPE                  44
D39V3, multiclass
                                                                                          clus
vv                                                                                         3P LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         3P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 7
  REGIONAL LYMPH NODE                                                                                     44
D39V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4    5
  3P LOSS WILD-TYPE   18   40
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               4                18
  MALE                 5                40
                   vv
clus                M0 M1 M1A M1B M1C
  3P LOSS MUTATED    7  0   0   0   0
  3P LOSS WILD-TYPE 49  1   1   1   2
D39V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  3P LOSS MUTATED    3  0   0   1   0   2   1  0  0
  3P LOSS WILD-TYPE 30  1   2   6   1   3   2  7  2
D39V6, multiclass
D39V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3P LOSS MUTATED             1       1        0        1        0         0
  3P LOSS WILD-TYPE           1       9        2        4        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3P LOSS MUTATED           0         1          0          2          1
  3P LOSS WILD-TYPE         2         4          2          5          8
                   vv
clus                STAGE IV
  3P LOSS MUTATED          0
  3P LOSS WILD-TYPE        3
D39V8, multiclass

Clustering(40) Variable = 3q loss mutation analysis
D40V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    4  5
  3Q LOSS WILD-TYPE 28 29
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9                57 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5                29 
$`3Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3C6 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-EE-A29H 
      112.54        58.03        36.03       176.55        61.18        32.19 
TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-GN-A262 
       48.59       101.26       120.46 

$`3Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       71.80       121.22        31.59        23.77        11.87        12.10 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I0 
       60.23         9.30       148.31         6.38       117.17        20.38 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 
       35.93       107.34        53.92       215.44        15.68        26.86 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
      109.64        78.87       168.26        63.32        47.84        39.62 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       44.35        56.42       345.96        58.75        47.54       135.91 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
      182.01        55.59        19.56        21.67       129.24        28.80 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP 
       19.76       103.27       103.17        16.96       144.76       248.61 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J 
      122.73         3.68        13.81        23.47       138.77         6.41 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
      228.59         7.76       357.37        53.52        15.45        32.71 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A265 
       11.41       148.77        84.72 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            32.19              3.68 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           176.55            357.37 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            61.18             53.92 
[1] "32.2 - 176.6 (61.2)" "3.7 - 357.4 (53.9)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D40V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3Q LOSS MUTATED                    0             0
  3Q LOSS WILD-TYPE                  6             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3Q LOSS MUTATED                                                                                          4
  3Q LOSS WILD-TYPE                                                                                        8
                   vv
clus                REGIONAL LYMPH NODE
  3Q LOSS MUTATED                     5
  3Q LOSS WILD-TYPE                  43
D40V3, multiclass
                                                                                          clus
vv                                                                                         3Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         3Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 8
  REGIONAL LYMPH NODE                                                                                     43
D40V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5    4
  3Q LOSS WILD-TYPE   17   41
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               5                17
  MALE                 4                41
                   vv
clus                M0 M1 M1A M1B M1C
  3Q LOSS MUTATED    8  0   0   0   0
  3Q LOSS WILD-TYPE 48  1   1   1   2
D40V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  3Q LOSS MUTATED    4  0   0   1   0   2   1  0  0
  3Q LOSS WILD-TYPE 29  1   2   6   1   3   2  7  2
D40V6, multiclass
D40V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3Q LOSS MUTATED             1       1        1        1        0         0
  3Q LOSS WILD-TYPE           1       9        1        4        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q LOSS MUTATED           0         1          0          2          1
  3Q LOSS WILD-TYPE         2         4          2          5          8
                   vv
clus                STAGE IV
  3Q LOSS MUTATED          0
  3Q LOSS WILD-TYPE        3
D40V8, multiclass

Clustering(41) Variable = 4p loss mutation analysis
D41V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    3  1
  4P LOSS WILD-TYPE 29 33
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                4                62 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                1                33 
$`4P LOSS MUTATED`
TCGA-D9-A148 TCGA-DA-A1HW TCGA-EE-A29C TCGA-EE-A3AG 
      148.31        36.03        47.84        23.47 

$`4P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HY 
       12.10        58.03        60.23         9.30         6.38       117.17 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
      215.44        15.68        26.86       109.64        78.87       168.26 
TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
       63.32        39.62        32.19        44.35        56.42       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT 
       58.75        47.54       135.91       182.01        55.59        19.56 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67       129.24        28.80        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF 
       16.96       144.76       248.61       122.73         3.68        13.81 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC 
      138.77         6.41        48.59       228.59         7.76       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
       53.52        15.45        32.71       101.26        11.41       148.77 
TCGA-GN-A262 TCGA-GN-A265 
      120.46        84.72 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            23.47              3.68 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           148.31            357.37 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           41.935            57.225 
[1] "23.5 - 148.3 (41.9)" "3.7 - 357.4 (57.2)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D41V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4P LOSS MUTATED                    0             0
  4P LOSS WILD-TYPE                  6             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4P LOSS MUTATED                                                                                          1
  4P LOSS WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  4P LOSS MUTATED                     3
  4P LOSS WILD-TYPE                  45
D41V3, multiclass
                                                                                          clus
vv                                                                                         4P LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         4P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     45
D41V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1    3
  4P LOSS WILD-TYPE   21   42
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               1                21
  MALE                 3                42
                   vv
clus                M0 M1 M1A M1B M1C
  4P LOSS MUTATED    2  0   0   1   0
  4P LOSS WILD-TYPE 54  1   1   0   2
D41V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  4P LOSS MUTATED    1  0   0   1   0   0   0  1  0
  4P LOSS WILD-TYPE 32  1   2   6   1   5   3  6  2
D41V6, multiclass
D41V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4P LOSS MUTATED             0       0        0        1        0         0
  4P LOSS WILD-TYPE           2      10        2        4        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P LOSS MUTATED           0         0          0          1          0
  4P LOSS WILD-TYPE         2         5          2          6          9
                   vv
clus                STAGE IV
  4P LOSS MUTATED          0
  4P LOSS WILD-TYPE        3
D41V8, multiclass
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                56 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HY        TCGA-DA-A1I0 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE        TCGA-EE-A2GH 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5        TCGA-EE-A2M6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME        TCGA-EE-A2MG 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP        TCGA-EE-A3AH 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19O        TCGA-FS-A1YX        TCGA-FS-A1YY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 

Clustering(42) Variable = 4q loss mutation analysis
D42V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    3  1
  4Q LOSS WILD-TYPE 29 33
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                62 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                33 
$`4Q LOSS MUTATED`
TCGA-D9-A148 TCGA-DA-A1HW TCGA-EE-A29C TCGA-EE-A3AG 
      148.31        36.03        47.84        23.47 

$`4Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HY 
       12.10        58.03        60.23         9.30         6.38       117.17 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
      215.44        15.68        26.86       109.64        78.87       168.26 
TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
       63.32        39.62        32.19        44.35        56.42       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT 
       58.75        47.54       135.91       182.01        55.59        19.56 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67       129.24        28.80        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF 
       16.96       144.76       248.61       122.73         3.68        13.81 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC 
      138.77         6.41        48.59       228.59         7.76       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
       53.52        15.45        32.71       101.26        11.41       148.77 
TCGA-GN-A262 TCGA-GN-A265 
      120.46        84.72 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            23.47              3.68 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           148.31            357.37 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           41.935            57.225 
[1] "23.5 - 148.3 (41.9)" "3.7 - 357.4 (57.2)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D42V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4Q LOSS MUTATED                    0             0
  4Q LOSS WILD-TYPE                  6             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4Q LOSS MUTATED                                                                                          1
  4Q LOSS WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  4Q LOSS MUTATED                     3
  4Q LOSS WILD-TYPE                  45
D42V3, multiclass
                                                                                          clus
vv                                                                                         4Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         4Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     45
D42V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    3
  4Q LOSS WILD-TYPE   21   42
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               1                21
  MALE                 3                42
                   vv
clus                M0 M1 M1A M1B M1C
  4Q LOSS MUTATED    2  0   0   1   0
  4Q LOSS WILD-TYPE 54  1   1   0   2
D42V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  4Q LOSS MUTATED    1  0   0   1   0   0   0  1  0
  4Q LOSS WILD-TYPE 32  1   2   6   1   5   3  6  2
D42V6, multiclass
D42V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4Q LOSS MUTATED             0       0        0        1        0         0
  4Q LOSS WILD-TYPE           2      10        2        4        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q LOSS MUTATED           0         0          0          1          0
  4Q LOSS WILD-TYPE         2         5          2          6          9
                   vv
clus                STAGE IV
  4Q LOSS MUTATED          0
  4Q LOSS WILD-TYPE        3
D42V8, multiclass
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                56 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HY        TCGA-DA-A1I0 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE        TCGA-EE-A2GH 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5        TCGA-EE-A2M6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME        TCGA-EE-A2MG 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP        TCGA-EE-A3AH 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19O        TCGA-FS-A1YX        TCGA-FS-A1YY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 

Clustering(43) Variable = 5p loss mutation analysis
D43V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    9  0
  5P LOSS WILD-TYPE 23 34
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9                57 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                0                34 
$`5P LOSS MUTATED`
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2GE TCGA-EE-A2GT TCGA-EE-A3AB 
       47.84        39.62        44.35       135.91        19.56       122.73 
TCGA-EE-A3AD TCGA-FS-A1ZM TCGA-GN-A262 
        3.68       101.26       120.46 

$`5P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX 
       12.10        58.03        60.23         9.30       148.31         6.38 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.17        20.38       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
       61.18        53.92       215.44        15.68        26.86       109.64 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T 
       78.87       168.26        63.32        32.19        56.42       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M6 
       58.75        47.54       182.01        55.59        21.67       129.24 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.80        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX 
      248.61        13.81        23.47       138.77         6.41        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
      228.59         7.76       357.37        53.52        15.45        32.71 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A265 
       11.41       148.77        84.72 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             3.68              6.38 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           135.91            357.37 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            47.84             56.42 
[1] "3.7 - 135.9 (47.8)" "6.4 - 357.4 (56.4)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "5P LOSS MUTATED"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "5P LOSS MUTATED"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "5P LOSS MUTATED"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
[1] "hr="     "8.3e+07"
D43V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5P LOSS MUTATED                    0             1
  5P LOSS WILD-TYPE                  6             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5P LOSS MUTATED                                                                                          2
  5P LOSS WILD-TYPE                                                                                       10
                   vv
clus                REGIONAL LYMPH NODE
  5P LOSS MUTATED                     6
  5P LOSS WILD-TYPE                  42
D43V3, multiclass
                                                                                          clus
vv                                                                                         5P LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    6
                                                                                          clus
vv                                                                                         5P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                10
  REGIONAL LYMPH NODE                                                                                     42
D43V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    7
  5P LOSS WILD-TYPE   20   38
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               2                20
  MALE                 7                38
                   vv
clus                M0 M1 M1A M1B M1C
  5P LOSS MUTATED    6  0   0   0   0
  5P LOSS WILD-TYPE 50  1   1   1   2
D43V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  5P LOSS MUTATED    4  0   0   1   0   0   1  0  0
  5P LOSS WILD-TYPE 29  1   2   6   1   5   2  7  2
D43V6, multiclass
D43V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5P LOSS MUTATED             0       1        0        2        0         1
  5P LOSS WILD-TYPE           2       9        2        3        8         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P LOSS MUTATED           0         1          0          1          0
  5P LOSS WILD-TYPE         2         4          2          6          9
                   vv
clus                STAGE IV
  5P LOSS MUTATED          0
  5P LOSS WILD-TYPE        3
D43V8, multiclass

Clustering(44) Variable = 5q loss mutation analysis
D44V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   13  7
  5Q LOSS WILD-TYPE 19 27
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               20                46 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7                27 
$`5Q LOSS MUTATED`
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 
       12.10        58.03         6.38        36.03        20.38       107.34 
TCGA-DA-A1I7 TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2GE 
       61.18       168.26        47.84        39.62        44.35       135.91 
TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AH TCGA-FS-A1YX 
       19.56       129.24       122.73         3.68       138.77        48.59 
TCGA-FS-A1ZM TCGA-GN-A262 
      101.26       120.46 

$`5Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 
       60.23         9.30       148.31       117.17       176.55        35.93 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       53.92       215.44        15.68        26.86       109.64        78.87 
TCGA-EE-A29A TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB 
       63.32        32.19        56.42       345.96        58.75        47.54 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME 
      182.01        55.59        21.67        28.80        19.76       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AF TCGA-EE-A3AG 
      103.17        16.96       144.76       248.61        13.81        23.47 
TCGA-ER-A19J TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
        6.41       228.59         7.76       357.37        53.52        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A265 
       32.71        11.41       148.77        84.72 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             3.68              6.41 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           168.26            357.37 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           53.310            56.005 
[1] "3.7 - 168.3 (53.3)" "6.4 - 357.4 (56.0)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D44V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5Q LOSS MUTATED                    2             1
  5Q LOSS WILD-TYPE                  4             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5Q LOSS MUTATED                                                                                          5
  5Q LOSS WILD-TYPE                                                                                        7
                   vv
clus                REGIONAL LYMPH NODE
  5Q LOSS MUTATED                    12
  5Q LOSS WILD-TYPE                  36
D44V3, multiclass
                                                                                          clus
vv                                                                                         5Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                   12
                                                                                          clus
vv                                                                                         5Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       4
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 7
  REGIONAL LYMPH NODE                                                                                     36
D44V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7   13
  5Q LOSS WILD-TYPE   15   32
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               7                15
  MALE                13                32
                   vv
clus                M0 M1 M1A M1B M1C
  5Q LOSS MUTATED   15  0   1   0   1
  5Q LOSS WILD-TYPE 41  1   0   1   1
D44V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  5Q LOSS MUTATED   10  0   0   2   0   2   1  1  1
  5Q LOSS WILD-TYPE 23  1   2   5   1   3   2  6  1
D44V6, multiclass
D44V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5Q LOSS MUTATED             0       4        0        3        1         1
  5Q LOSS WILD-TYPE           2       6        2        2        7         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q LOSS MUTATED           0         1          0          3          2
  5Q LOSS WILD-TYPE         2         4          2          4          7
                   vv
clus                STAGE IV
  5Q LOSS MUTATED          1
  5Q LOSS WILD-TYPE        2
D44V8, multiclass

Clustering(45) Variable = 6p loss mutation analysis
D45V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED    2  4
  6P LOSS WILD-TYPE 30 30
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                60 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4                30 
$`6P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-DA-A1I8 TCGA-EE-A29M TCGA-FS-A1YX TCGA-FS-A1ZS 
      112.54        31.59        53.92        44.35        48.59       148.77 

$`6P LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       71.80       121.22        23.77        11.87        12.10        58.03 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY 
       60.23         9.30       148.31         6.38        36.03       117.17 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 
       20.38       176.55        35.93       107.34        61.18       215.44 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       15.68        26.86       109.64        78.87       168.26        63.32 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       47.84        39.62        32.19        56.42       345.96        58.75 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       47.54       135.91       182.01        55.59        19.56        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
      129.24        28.80        19.76       103.27       103.17        16.96 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      144.76       248.61       122.73         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      138.77         6.41       228.59         7.76       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
       15.45        32.71       101.26        11.41       120.46        84.72 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            31.59              3.68 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           148.77            357.37 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           51.255            57.225 
[1] "31.6 - 148.8 (51.3)" "3.7 - 357.4 (57.2)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D45V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6P LOSS MUTATED                    0             1
  6P LOSS WILD-TYPE                  6             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6P LOSS MUTATED                                                                                          2
  6P LOSS WILD-TYPE                                                                                       10
                   vv
clus                REGIONAL LYMPH NODE
  6P LOSS MUTATED                     3
  6P LOSS WILD-TYPE                  45
D45V3, multiclass
                                                                                          clus
vv                                                                                         6P LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         6P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                10
  REGIONAL LYMPH NODE                                                                                     45
D45V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3    3
  6P LOSS WILD-TYPE   19   42
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               3                19
  MALE                 3                42
                   vv
clus                M0 M1 M1A M1B M1C
  6P LOSS MUTATED    6  0   0   0   0
  6P LOSS WILD-TYPE 50  1   1   1   2
D45V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  6P LOSS MUTATED    4  0   0   0   1   0   0  1  0
  6P LOSS WILD-TYPE 29  1   2   7   0   5   3  6  2
D45V6, multiclass
D45V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6P LOSS MUTATED             1       1        0        1        1         0
  6P LOSS WILD-TYPE           1       9        2        4        7         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P LOSS MUTATED           0         0          0          1          1
  6P LOSS WILD-TYPE         2         5          2          6          8
                   vv
clus                STAGE IV
  6P LOSS MUTATED          0
  6P LOSS WILD-TYPE        3
D45V8, multiclass

Clustering(46) Variable = 6q loss mutation analysis
D46V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   16 14
  6Q LOSS WILD-TYPE 16 20
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               30                36 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               14                20 
$`6Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HY 
      112.54        31.59        58.03       148.31         6.38       117.17 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A183 TCGA-EE-A20B 
       35.93        61.18        53.92       215.44        26.86       109.64 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2A6 
      168.26        63.32        47.84        32.19        44.35        58.75 
TCGA-EE-A2GB TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A3AD TCGA-EE-A3AG TCGA-ER-A19J 
       47.54       129.24        28.80         3.68        23.47         6.41 
TCGA-FS-A1YX TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
       48.59        15.45        32.71       101.26        11.41       148.77 

$`6Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CE 
       71.80       121.22        23.77        11.87        12.10        60.23 
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A3F8 
        9.30        36.03        20.38       176.55       107.34        15.68 
TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2GE TCGA-EE-A2GH 
       78.87        39.62        56.42       345.96       135.91       182.01 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       55.59        19.56        21.67        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AF TCGA-EE-A3AH 
       16.96       144.76       248.61       122.73        13.81       138.77 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-GN-A262 TCGA-GN-A265 
      228.59         7.76       357.37        53.52       120.46        84.72 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             3.68              7.76 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           215.44            357.37 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           48.215            66.015 
[1] "3.7 - 215.4 (48.2)" "7.8 - 357.4 (66.0)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D46V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6Q LOSS MUTATED                    3             1
  6Q LOSS WILD-TYPE                  3             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6Q LOSS MUTATED                                                                                          8
  6Q LOSS WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  6Q LOSS MUTATED                    19
  6Q LOSS WILD-TYPE                  29
D46V3, multiclass
                                                                                          clus
vv                                                                                         6Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     3
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               8
  REGIONAL LYMPH NODE                                                                                   19
                                                                                          clus
vv                                                                                         6Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       3
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                     29
D46V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      9   22
  6Q LOSS WILD-TYPE   13   23
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               9                13
  MALE                22                23
                   vv
clus                M0 M1 M1A M1B M1C
  6Q LOSS MUTATED   26  1   0   1   1
  6Q LOSS WILD-TYPE 30  0   1   0   1
D46V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  6Q LOSS MUTATED   15  0   2   1   1   2   2  5  1
  6Q LOSS WILD-TYPE 18  1   0   6   0   3   1  2  1
D46V6, multiclass
D46V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6Q LOSS MUTATED             1       4        2        3        4         0
  6Q LOSS WILD-TYPE           1       6        0        2        4         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q LOSS MUTATED           1         1          2          4          3
  6Q LOSS WILD-TYPE         1         4          0          3          6
                   vv
clus                STAGE IV
  6Q LOSS MUTATED          2
  6Q LOSS WILD-TYPE        1
D46V8, multiclass

Clustering(47) Variable = 8p loss mutation analysis
D47V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    3  4
  8P LOSS WILD-TYPE 29 30
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                7                59 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                30 
$`8P LOSS MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 TCGA-EE-A183 TCGA-EE-A29C TCGA-EE-A29H 
       58.03         9.30       148.31        26.86        47.84        32.19 
TCGA-FS-A1YY 
      228.59 

$`8P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       12.10        60.23         6.38        36.03       117.17        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
      176.55        35.93       107.34        61.18        53.92       215.44 
TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E 
       15.68       109.64        78.87       168.26        63.32        39.62 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       44.35        56.42       345.96        58.75        47.54       135.91 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
      182.01        55.59        19.56        21.67       129.24        28.80 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP 
       19.76       103.27       103.17        16.96       144.76       248.61 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J 
      122.73         3.68        13.81        23.47       138.77         6.41 
TCGA-FS-A1YX TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
       48.59         7.76       357.37        53.52        15.45        32.71 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
      101.26        11.41       148.77       120.46        84.72 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             9.30              3.68 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           228.59            357.37 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            47.84             56.42 
[1] "9.3 - 228.6 (47.8)" "3.7 - 357.4 (56.4)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D47V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8P LOSS MUTATED                    1             0
  8P LOSS WILD-TYPE                  5             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8P LOSS MUTATED                                                                                          1
  8P LOSS WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  8P LOSS MUTATED                     5
  8P LOSS WILD-TYPE                  43
D47V3, multiclass
                                                                                          clus
vv                                                                                         8P LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         8P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     43
D47V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3    4
  8P LOSS WILD-TYPE   19   41
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               3                19
  MALE                 4                41
                   vv
clus                M0 M1 M1A M1B M1C
  8P LOSS MUTATED    6  0   0   1   0
  8P LOSS WILD-TYPE 50  1   1   0   2
D47V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  8P LOSS MUTATED    5  0   0   0   0   0   1  1  0
  8P LOSS WILD-TYPE 28  1   2   7   1   5   2  6  2
D47V6, multiclass
D47V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8P LOSS MUTATED             0       1        1        2        0         1
  8P LOSS WILD-TYPE           2       9        1        3        8         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P LOSS MUTATED           0         1          0          0          0
  8P LOSS WILD-TYPE         2         4          2          7          9
                   vv
clus                STAGE IV
  8P LOSS MUTATED          0
  8P LOSS WILD-TYPE        3
D47V8, multiclass

Clustering(48) Variable = 9p loss mutation analysis
D48V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   17 20
  9P LOSS WILD-TYPE 15 14
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               37                29 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               20                14 
$`9P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 
      112.54        71.80        12.10        58.03         9.30       148.31 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       36.03       117.17       176.55        35.93       107.34        53.92 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29P 
      109.64        78.87       168.26        47.84        39.62        56.42 
TCGA-EE-A2GB TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A3AB 
       47.54        55.59       129.24        16.96       144.76       122.73 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-FS-A1YX TCGA-FS-A1YY 
        3.68        13.81        23.47       138.77        48.59       228.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR 
        7.76       357.37        15.45        32.71       101.26        11.41 
TCGA-FS-A1ZS 
      148.77 

$`9P LOSS WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D9-A1JX 
      121.22        31.59        23.77        11.87        60.23         6.38 
TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A29A 
       20.38        61.18       215.44        15.68        26.86        63.32 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH 
       32.19        44.35       345.96        58.75       135.91       182.01 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       19.56        21.67        28.80        19.76       103.27       103.17 
TCGA-EE-A2MP TCGA-ER-A19J TCGA-FS-A1ZD TCGA-GN-A262 TCGA-GN-A265 
      248.61         6.41        53.52       120.46        84.72 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             3.68              6.38 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           357.37            345.96 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            56.42             53.52 
[1] "3.7 - 357.4 (56.4)" "6.4 - 346.0 (53.5)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D48V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9P LOSS MUTATED                    5             0
  9P LOSS WILD-TYPE                  1             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9P LOSS MUTATED                                                                                          9
  9P LOSS WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  9P LOSS MUTATED                    24
  9P LOSS WILD-TYPE                  24
D48V3, multiclass
                                                                                          clus
vv                                                                                         9P LOSS MUTATED
  DISTANT METASTASIS                                                                                     5
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               9
  REGIONAL LYMPH NODE                                                                                   24
                                                                                          clus
vv                                                                                         9P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       1
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     24
D48V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     13   25
  9P LOSS WILD-TYPE    9   20
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              13                 9
  MALE                25                20
                   vv
clus                M0 M1 M1A M1B M1C
  9P LOSS MUTATED   31  0   0   1   2
  9P LOSS WILD-TYPE 25  1   1   0   0
D48V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  9P LOSS MUTATED   19  0   1   5   0   3   3  3  0
  9P LOSS WILD-TYPE 14  1   1   2   1   2   0  4  2
D48V6, multiclass
D48V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9P LOSS MUTATED             2       3        0        3        7         1
  9P LOSS WILD-TYPE           0       7        2        2        1         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9P LOSS MUTATED           2         3          1          4          5
  9P LOSS WILD-TYPE         0         2          1          3          4
                   vv
clus                STAGE IV
  9P LOSS MUTATED          2
  9P LOSS WILD-TYPE        1
D48V8, multiclass

Clustering(49) Variable = 9q loss mutation analysis
D49V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   15 14
  9Q LOSS WILD-TYPE 17 20
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               29                37 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               14                20 
$`9Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3C6 TCGA-D9-A148 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 
      112.54        58.03       148.31        36.03       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29P 
      107.34        53.92       109.64        78.87       168.26        56.42 
TCGA-EE-A2GB TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A3AB 
       47.54        55.59       129.24        16.96       144.76       122.73 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZF 
        3.68        13.81        23.47       228.59       357.37        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
       32.71       101.26        11.41       148.77       120.46 

$`9Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       71.80       121.22        31.59        23.77        11.87        12.10 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I7 
       60.23         9.30         6.38       117.17        20.38        61.18 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
      215.44        15.68        26.86        63.32        47.84        39.62 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GH 
       32.19        44.35       345.96        58.75       135.91       182.01 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       19.56        21.67        28.80        19.76       103.27       103.17 
TCGA-EE-A2MP TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1Z7 TCGA-FS-A1ZD 
      248.61       138.77         6.41        48.59         7.76        53.52 
TCGA-GN-A265 
       84.72 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             3.68              6.38 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           357.37            345.96 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            78.87             47.84 
[1] "3.7 - 357.4 (78.9)" "6.4 - 346.0 (47.8)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-GN-A262        TCGA-GN-A265 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D49V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9Q LOSS MUTATED                    5             0
  9Q LOSS WILD-TYPE                  1             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9Q LOSS MUTATED                                                                                          7
  9Q LOSS WILD-TYPE                                                                                        5
                   vv
clus                REGIONAL LYMPH NODE
  9Q LOSS MUTATED                    17
  9Q LOSS WILD-TYPE                  31
D49V3, multiclass
                                                                                          clus
vv                                                                                         9Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     5
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   17
                                                                                          clus
vv                                                                                         9Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       1
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 5
  REGIONAL LYMPH NODE                                                                                     31
D49V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     13   16
  9Q LOSS WILD-TYPE    9   29
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              13                 9
  MALE                16                29
                   vv
clus                M0 M1 M1A M1B M1C
  9Q LOSS MUTATED   21  0   0   1   2
  9Q LOSS WILD-TYPE 35  1   1   0   0
D49V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  9Q LOSS MUTATED   16  0   1   1   0   2   2  2  0
  9Q LOSS WILD-TYPE 17  1   1   6   1   3   1  5  2
D49V6, multiclass
D49V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9Q LOSS MUTATED             2       2        0        2        6         1
  9Q LOSS WILD-TYPE           0       8        2        3        2         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q LOSS MUTATED           2         1          1          2          2
  9Q LOSS WILD-TYPE         0         4          1          5          7
                   vv
clus                STAGE IV
  9Q LOSS MUTATED          2
  9Q LOSS WILD-TYPE        1
D49V8, multiclass

Clustering(50) Variable = 10p loss mutation analysis
D50V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   16 20
  10P LOSS WILD-TYPE 16 14
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                36                 30 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                20                 14 
$`10P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3MO 
      112.54        71.80       121.22        12.10        60.23         9.30 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       36.03       176.55        35.93       107.34        61.18        53.92 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
      109.64        78.87       168.26        32.19        44.35        56.42 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MH 
       47.54       135.91        55.59       129.24        28.80        16.96 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AH TCGA-FS-A1YX TCGA-FS-A1Z7 
      144.76       248.61         3.68       138.77        48.59         7.76 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR 
      357.37        53.52        15.45        32.71       101.26        11.41 

$`10P LOSS WILD-TYPE`
TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3C6 TCGA-D9-A148 TCGA-D9-A1JX 
       31.59        23.77        11.87        58.03       148.31         6.38 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A29A 
      117.17        20.38       215.44        15.68        26.86        63.32 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GT 
       47.84        39.62       345.96        58.75       182.01        19.56 
TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A3AB TCGA-EE-A3AF 
       21.67        19.76       103.27       103.17       122.73        13.81 
TCGA-EE-A3AG TCGA-ER-A19J TCGA-FS-A1YY TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       23.47         6.41       228.59       148.77       120.46        84.72 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              3.68               6.38 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            357.37             345.96 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            56.005             52.935 
[1] "3.7 - 357.4 (56.0)" "6.4 - 346.0 (52.9)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D50V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10P LOSS MUTATED                    4             1
  10P LOSS WILD-TYPE                  2             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  10P LOSS MUTATED                                                                                          9
  10P LOSS WILD-TYPE                                                                                        3
                    vv
clus                 REGIONAL LYMPH NODE
  10P LOSS MUTATED                    22
  10P LOSS WILD-TYPE                  26
D50V3, multiclass
                                                                                          clus
vv                                                                                         10P LOSS MUTATED
  DISTANT METASTASIS                                                                                      4
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                9
  REGIONAL LYMPH NODE                                                                                    22
                                                                                          clus
vv                                                                                         10P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        2
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  3
  REGIONAL LYMPH NODE                                                                                      26
D50V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     15   21
  10P LOSS WILD-TYPE    7   24
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               15                  7
  MALE                 21                 24
                    vv
clus                 M0 M1 M1A M1B M1C
  10P LOSS MUTATED   33  0   0   0   2
  10P LOSS WILD-TYPE 23  1   1   1   0
D50V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  10P LOSS MUTATED   22  0   1   4   0   4   3  1  0
  10P LOSS WILD-TYPE 11  1   1   3   1   1   0  6  2
D50V6, multiclass
D50V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  10P LOSS MUTATED             2       5        1        3        7         1
  10P LOSS WILD-TYPE           0       5        1        2        1         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  10P LOSS MUTATED           2         4          1          3          4
  10P LOSS WILD-TYPE         0         1          1          4          5
                    vv
clus                 STAGE IV
  10P LOSS MUTATED          2
  10P LOSS WILD-TYPE        1
D50V8, multiclass

Clustering(51) Variable = 10q loss mutation analysis
D51V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   21 24
  10Q LOSS WILD-TYPE 11 10
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                45                 21 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                24                 10 
$`10Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2JK TCGA-D3-A3C6 
      112.54        71.80       121.22        31.59        12.10        58.03 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 
       60.23         9.30       148.31        36.03       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A20F 
      107.34        61.18        53.92        15.68       109.64        78.87 
TCGA-EE-A20H TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A6 TCGA-EE-A2GB 
      168.26        32.19        44.35        56.42        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2MK 
      135.91        55.59       129.24        28.80        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-FS-A1YX 
      248.61         3.68        13.81        23.47       138.77        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
      228.59         7.76       357.37        53.52        15.45        32.71 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-GN-A262 
      101.26        11.41       120.46 

$`10Q LOSS WILD-TYPE`
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A3F5 
       23.77        11.87         6.38       117.17        20.38       215.44 
TCGA-EE-A183 TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29T TCGA-EE-A2GH 
       26.86        63.32        47.84        39.62       345.96       182.01 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A3AB 
       19.56        21.67        19.76       103.27       103.17       122.73 
TCGA-ER-A19J TCGA-FS-A1ZS TCGA-GN-A265 
        6.41       148.77        84.72 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              3.68               6.38 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            357.37             345.96 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             56.42              47.84 
[1] "3.7 - 357.4 (56.4)" "6.4 - 346.0 (47.8)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D51V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10Q LOSS MUTATED                    5             1
  10Q LOSS WILD-TYPE                  1             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  10Q LOSS MUTATED                                                                                         11
  10Q LOSS WILD-TYPE                                                                                        1
                    vv
clus                 REGIONAL LYMPH NODE
  10Q LOSS MUTATED                    28
  10Q LOSS WILD-TYPE                  20
D51V3, multiclass
                                                                                          clus
vv                                                                                         10Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      5
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               11
  REGIONAL LYMPH NODE                                                                                    28
                                                                                          clus
vv                                                                                         10Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        1
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  1
  REGIONAL LYMPH NODE                                                                                      20
D51V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     19   26
  10Q LOSS WILD-TYPE    3   19
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               19                  3
  MALE                 26                 19
                    vv
clus                 M0 M1 M1A M1B M1C
  10Q LOSS MUTATED   38  0   0   1   2
  10Q LOSS WILD-TYPE 18  1   1   0   0
D51V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  10Q LOSS MUTATED   25  0   1   4   1   5   3  2  0
  10Q LOSS WILD-TYPE  8  1   1   3   0   0   0  5  2
D51V6, multiclass
D51V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  10Q LOSS MUTATED             2       5        2        4        7         2
  10Q LOSS WILD-TYPE           0       5        0        1        1         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  10Q LOSS MUTATED           2         4          1          5          4
  10Q LOSS WILD-TYPE         0         1          1          2          5
                    vv
clus                 STAGE IV
  10Q LOSS MUTATED          2
  10Q LOSS WILD-TYPE        1
D51V8, multiclass

Clustering(52) Variable = 11p loss mutation analysis
D52V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    7  6
  11P LOSS WILD-TYPE 25 28
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                13                 53 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 6                 28 
$`11P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1I5 
      112.54        31.59         9.30         6.38        36.03       107.34 
TCGA-DA-A1I8 TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A3AB TCGA-EE-A3AD TCGA-FS-A1ZH 
       53.92        47.84        44.35       122.73         3.68        32.71 
TCGA-GN-A262 
      120.46 

$`11P LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       71.80       121.22        23.77        11.87        12.10        58.03 
TCGA-D3-A3CE TCGA-D9-A148 TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       60.23       148.31       117.17        20.38       176.55        35.93 
TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       61.18       215.44        15.68        26.86       109.64        78.87 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T 
      168.26        63.32        39.62        32.19        56.42       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT 
       58.75        47.54       135.91       182.01        55.59        19.56 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67       129.24        28.80        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
       16.96       144.76       248.61        13.81        23.47       138.77 
TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
        6.41        48.59       228.59         7.76       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A265 
       15.45       101.26        11.41       148.77        84.72 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              3.68               6.41 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            122.73             357.37 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             44.35              58.75 
[1] "3.7 - 122.7 (44.4)" "6.4 - 357.4 (58.8)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D52V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11P LOSS MUTATED                    1             1
  11P LOSS WILD-TYPE                  5             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11P LOSS MUTATED                                                                                          3
  11P LOSS WILD-TYPE                                                                                        9
                    vv
clus                 REGIONAL LYMPH NODE
  11P LOSS MUTATED                     8
  11P LOSS WILD-TYPE                  40
D52V3, multiclass
                                                                                          clus
vv                                                                                         11P LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     8
                                                                                          clus
vv                                                                                         11P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  9
  REGIONAL LYMPH NODE                                                                                      40
D52V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      7    6
  11P LOSS WILD-TYPE   15   39
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                7                 15
  MALE                  6                 39
                    vv
clus                 M0 M1 M1A M1B M1C
  11P LOSS MUTATED    8  0   0   0   2
  11P LOSS WILD-TYPE 48  1   1   1   0
D52V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  11P LOSS MUTATED    4  0   0   1   1   0   2  1  1
  11P LOSS WILD-TYPE 29  1   2   6   0   5   1  6  1
D52V6, multiclass
D52V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11P LOSS MUTATED             1       0        0        2        0         0
  11P LOSS WILD-TYPE           1      10        2        3        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  11P LOSS MUTATED           0         1          0          2          1
  11P LOSS WILD-TYPE         2         4          2          5          8
                    vv
clus                 STAGE IV
  11P LOSS MUTATED          2
  11P LOSS WILD-TYPE        1
D52V8, multiclass

Clustering(53) Variable = 11q loss mutation analysis
D53V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    7  8
  11Q LOSS WILD-TYPE 25 26
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                15                 51 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 8                 26 
$`11Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HW 
      112.54       121.22        31.59         9.30         6.38        36.03 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A3AB TCGA-EE-A3AD 
      107.34        53.92        47.84        44.35       122.73         3.68 
TCGA-FS-A1Z7 TCGA-FS-A1ZF TCGA-FS-A1ZH 
        7.76        15.45        32.71 

$`11Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
       71.80        23.77        11.87        12.10        58.03        60.23 
TCGA-D9-A148 TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
      148.31       117.17        20.38       176.55        35.93        61.18 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
      215.44        15.68        26.86       109.64        78.87       168.26 
TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       63.32        39.62        32.19        56.42       345.96        58.75 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       47.54       135.91       182.01        55.59        19.56        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
      129.24        28.80        19.76       103.27       103.17        16.96 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J 
      144.76       248.61        13.81        23.47       138.77         6.41 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZR 
       48.59       228.59       357.37        53.52       101.26        11.41 
TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
      148.77       120.46        84.72 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              3.68               6.41 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            122.73             357.37 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             36.03              60.23 
[1] "3.7 - 122.7 (36.0)" "6.4 - 357.4 (60.2)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D53V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11Q LOSS MUTATED                    2             1
  11Q LOSS WILD-TYPE                  4             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11Q LOSS MUTATED                                                                                          2
  11Q LOSS WILD-TYPE                                                                                       10
                    vv
clus                 REGIONAL LYMPH NODE
  11Q LOSS MUTATED                    10
  11Q LOSS WILD-TYPE                  38
D53V3, multiclass
                                                                                          clus
vv                                                                                         11Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                    10
                                                                                          clus
vv                                                                                         11Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        4
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 10
  REGIONAL LYMPH NODE                                                                                      38
D53V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      8    7
  11Q LOSS WILD-TYPE   14   38
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                8                 14
  MALE                  7                 38
                    vv
clus                 M0 M1 M1A M1B M1C
  11Q LOSS MUTATED   11  0   0   0   2
  11Q LOSS WILD-TYPE 45  1   1   1   0
D53V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  11Q LOSS MUTATED    6  0   0   2   1   0   2  1  1
  11Q LOSS WILD-TYPE 27  1   2   5   0   5   1  6  1
D53V6, multiclass
D53V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11Q LOSS MUTATED             1       0        0        3        0         0
  11Q LOSS WILD-TYPE           1      10        2        2        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  11Q LOSS MUTATED           1         1          0          2          2
  11Q LOSS WILD-TYPE         1         4          2          5          7
                    vv
clus                 STAGE IV
  11Q LOSS MUTATED          2
  11Q LOSS WILD-TYPE        1
D53V8, multiclass

Clustering(54) Variable = 12p loss mutation analysis
D54V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    1  2
  12P LOSS WILD-TYPE 31 32
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                 63 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                 32 
$`12P LOSS MUTATED`
TCGA-EE-A2MK TCGA-FS-A1YX TCGA-FS-A1ZH 
      144.76        48.59        32.71 

$`12P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX 
       12.10        58.03        60.23         9.30       148.31         6.38 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.17        20.38       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
       61.18        53.92       215.44        15.68        26.86       109.64 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       78.87       168.26        63.32        47.84        39.62        32.19 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       44.35        56.42       345.96        58.75        47.54       135.91 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
      182.01        55.59        19.56        21.67       129.24        28.80 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A3AB 
       19.76       103.27       103.17        16.96       248.61       122.73 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YY 
        3.68        13.81        23.47       138.77         6.41       228.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZR 
        7.76       357.37        53.52        15.45       101.26        11.41 
TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
      148.77       120.46        84.72 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             32.71               3.68 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            144.76             357.37 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             48.59              56.42 
[1] "32.7 - 144.8 (48.6)" "3.7 - 357.4 (56.4)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D54V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12P LOSS MUTATED                    0             0
  12P LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12P LOSS MUTATED                                                                                          1
  12P LOSS WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  12P LOSS MUTATED                     2
  12P LOSS WILD-TYPE                  46
D54V3, multiclass
                                                                                          clus
vv                                                                                         12P LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         12P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      46
D54V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    0
  12P LOSS WILD-TYPE   19   45
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                3                 19
  MALE                  0                 45
                    vv
clus                 M0 M1 M1A M1B M1C
  12P LOSS MUTATED    2  0   0   0   1
  12P LOSS WILD-TYPE 54  1   1   1   1
D54V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  12P LOSS MUTATED    2  0   0   0   0   0   1  0  0
  12P LOSS WILD-TYPE 31  1   2   7   1   5   2  7  2
D54V6, multiclass
D54V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12P LOSS MUTATED             0       1        0        0        1         0
  12P LOSS WILD-TYPE           2       9        2        5        7         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  12P LOSS MUTATED           0         0          0          0          0
  12P LOSS WILD-TYPE         2         5          2          7          9
                    vv
clus                 STAGE IV
  12P LOSS MUTATED          1
  12P LOSS WILD-TYPE        2
D54V8, multiclass

Clustering(55) Variable = 12q loss mutation analysis
D55V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    2  2
  12Q LOSS WILD-TYPE 30 32
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 62 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                 32 
$`12Q LOSS MUTATED`
TCGA-EE-A2MK TCGA-EE-A3AD TCGA-FS-A1YX TCGA-FS-A1ZH 
      144.76         3.68        48.59        32.71 

$`12Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX 
       12.10        58.03        60.23         9.30       148.31         6.38 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.17        20.38       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
       61.18        53.92       215.44        15.68        26.86       109.64 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       78.87       168.26        63.32        47.84        39.62        32.19 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       44.35        56.42       345.96        58.75        47.54       135.91 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
      182.01        55.59        19.56        21.67       129.24        28.80 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A3AB 
       19.76       103.27       103.17        16.96       248.61       122.73 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YY TCGA-FS-A1Z7 
       13.81        23.47       138.77         6.41       228.59         7.76 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
      357.37        53.52        15.45       101.26        11.41       148.77 
TCGA-GN-A262 TCGA-GN-A265 
      120.46        84.72 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              3.68               6.38 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            144.76             357.37 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            40.650             57.225 
[1] "3.7 - 144.8 (40.7)" "6.4 - 357.4 (57.2)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D55V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12Q LOSS MUTATED                    0             0
  12Q LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12Q LOSS MUTATED                                                                                          1
  12Q LOSS WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  12Q LOSS MUTATED                     3
  12Q LOSS WILD-TYPE                  45
D55V3, multiclass
                                                                                          clus
vv                                                                                         12Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         12Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      45
D55V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    1
  12Q LOSS WILD-TYPE   19   44
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                3                 19
  MALE                  1                 44
                    vv
clus                 M0 M1 M1A M1B M1C
  12Q LOSS MUTATED    2  0   0   0   1
  12Q LOSS WILD-TYPE 54  1   1   1   1
D55V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  12Q LOSS MUTATED    2  0   0   0   0   0   1  0  0
  12Q LOSS WILD-TYPE 31  1   2   7   1   5   2  7  2
D55V6, multiclass
D55V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12Q LOSS MUTATED             0       1        0        0        1         0
  12Q LOSS WILD-TYPE           2       9        2        5        7         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  12Q LOSS MUTATED           0         0          0          0          0
  12Q LOSS WILD-TYPE         2         5          2          7          9
                    vv
clus                 STAGE IV
  12Q LOSS MUTATED          1
  12Q LOSS WILD-TYPE        2
D55V8, multiclass

Clustering(56) Variable = 13q loss mutation analysis
D56V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    5  5
  13Q LOSS WILD-TYPE 27 29
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                10                 56 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                 29 
$`13Q LOSS MUTATED`
TCGA-D9-A148 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-EE-A29C TCGA-EE-A29M 
      148.31       176.55        35.93        53.92        47.84        44.35 
TCGA-EE-A29T TCGA-EE-A3AD TCGA-EE-A3AH TCGA-FS-A1ZH 
      345.96         3.68       138.77        32.71 

$`13Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HW 
       12.10        58.03        60.23         9.30         6.38        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 
      117.17        20.38       107.34        61.18       215.44        15.68 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E 
       26.86       109.64        78.87       168.26        63.32        39.62 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
       32.19        56.42        58.75        47.54       135.91       182.01 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.59        19.56        21.67       129.24        28.80        19.76 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB 
      103.27       103.17        16.96       144.76       248.61       122.73 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
       13.81        23.47         6.41        48.59       228.59         7.76 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
      357.37        53.52        15.45       101.26        11.41       148.77 
TCGA-GN-A262 TCGA-GN-A265 
      120.46        84.72 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              3.68               6.38 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            345.96             357.37 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            50.880             57.225 
[1] "3.7 - 346.0 (50.9)" "6.4 - 357.4 (57.2)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D56V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  13Q LOSS MUTATED                    0             1
  13Q LOSS WILD-TYPE                  6             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  13Q LOSS MUTATED                                                                                          2
  13Q LOSS WILD-TYPE                                                                                       10
                    vv
clus                 REGIONAL LYMPH NODE
  13Q LOSS MUTATED                     7
  13Q LOSS WILD-TYPE                  41
D56V3, multiclass
                                                                                          clus
vv                                                                                         13Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         13Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 10
  REGIONAL LYMPH NODE                                                                                      41
D56V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4    6
  13Q LOSS WILD-TYPE   18   39
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                4                 18
  MALE                  6                 39
                    vv
clus                 M0 M1 M1A M1B M1C
  13Q LOSS MUTATED    7  0   0   1   1
  13Q LOSS WILD-TYPE 49  1   1   0   1
D56V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  13Q LOSS MUTATED    3  0   0   0   0   2   1  2  1
  13Q LOSS WILD-TYPE 30  1   2   7   1   3   2  5  1
D56V6, multiclass
D56V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  13Q LOSS MUTATED             0       0        0        2        1         0
  13Q LOSS WILD-TYPE           2      10        2        3        7         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  13Q LOSS MUTATED           0         0          0          1          2
  13Q LOSS WILD-TYPE         2         5          2          6          7
                    vv
clus                 STAGE IV
  13Q LOSS MUTATED          1
  13Q LOSS WILD-TYPE        2
D56V8, multiclass

Clustering(57) Variable = 14q loss mutation analysis
D57V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED    9  9
  14Q LOSS WILD-TYPE 23 25
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                18                 48 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 9                 25 
$`14Q LOSS MUTATED`
TCGA-D3-A3CE TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-EE-A29C TCGA-EE-A2A6 
       60.23       117.17       107.34       215.44        47.84        58.75 
TCGA-EE-A2GE TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A3AH 
      135.91       129.24        28.80        16.96       144.76       138.77 
TCGA-FS-A1YX TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR 
       48.59         7.76       357.37        32.71       101.26        11.41 

$`14Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       12.10        58.03         9.30       148.31         6.38        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 
       20.38       176.55        35.93        61.18        53.92        15.68 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E 
       26.86       109.64        78.87       168.26        63.32        39.62 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2GB TCGA-EE-A2GH 
       32.19        44.35        56.42       345.96        47.54       182.01 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       55.59        19.56        21.67        19.76       103.27       103.17 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-ER-A19J 
      248.61       122.73         3.68        13.81        23.47         6.41 
TCGA-FS-A1YY TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
      228.59        53.52        15.45       148.77       120.46        84.72 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              7.76               3.68 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            357.37             345.96 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            80.745             53.720 
[1] "7.8 - 357.4 (80.7)" "3.7 - 346.0 (53.7)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D57V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  14Q LOSS MUTATED                    2             0
  14Q LOSS WILD-TYPE                  4             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  14Q LOSS MUTATED                                                                                          3
  14Q LOSS WILD-TYPE                                                                                        9
                    vv
clus                 REGIONAL LYMPH NODE
  14Q LOSS MUTATED                    13
  14Q LOSS WILD-TYPE                  35
D57V3, multiclass
                                                                                          clus
vv                                                                                         14Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                    13
                                                                                          clus
vv                                                                                         14Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        4
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  9
  REGIONAL LYMPH NODE                                                                                      35
D57V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      5   13
  14Q LOSS WILD-TYPE   17   32
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                5                 17
  MALE                 13                 32
                    vv
clus                 M0 M1 M1A M1B M1C
  14Q LOSS MUTATED   16  0   0   0   2
  14Q LOSS WILD-TYPE 40  1   1   1   0
D57V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  14Q LOSS MUTATED   12  0   0   2   0   0   2  2  0
  14Q LOSS WILD-TYPE 21  1   2   5   1   5   1  5  2
D57V6, multiclass
D57V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  14Q LOSS MUTATED             1       3        1        1        5         0
  14Q LOSS WILD-TYPE           1       7        1        4        3         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  14Q LOSS MUTATED           0         2          0          0          3
  14Q LOSS WILD-TYPE         2         3          2          7          6
                    vv
clus                 STAGE IV
  14Q LOSS MUTATED          2
  14Q LOSS WILD-TYPE        1
D57V8, multiclass

Clustering(58) Variable = 15q loss mutation analysis
D58V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    4  2
  15Q LOSS WILD-TYPE 28 32
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 60 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 32 
$`15Q LOSS MUTATED`
TCGA-D3-A3C6 TCGA-D9-A148 TCGA-EE-A29P TCGA-EE-A2MK TCGA-FS-A1YX TCGA-FS-A1ZM 
       58.03       148.31        56.42       144.76        48.59       101.26 

$`15Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY 
       12.10        60.23         9.30         6.38        36.03       117.17 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
      215.44        15.68        26.86       109.64        78.87       168.26 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T 
       63.32        47.84        39.62        32.19        44.35       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT 
       58.75        47.54       135.91       182.01        55.59        19.56 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67       129.24        28.80        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
       16.96       248.61       122.73         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      138.77         6.41       228.59         7.76       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       15.45        32.71        11.41       148.77       120.46        84.72 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             48.59               3.68 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            148.31             357.37 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            79.645             53.720 
[1] "48.6 - 148.3 (79.6)" "3.7 - 357.4 (53.7)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D58V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  15Q LOSS MUTATED                    0             0
  15Q LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  15Q LOSS MUTATED                                                                                          2
  15Q LOSS WILD-TYPE                                                                                       10
                    vv
clus                 REGIONAL LYMPH NODE
  15Q LOSS MUTATED                     4
  15Q LOSS WILD-TYPE                  44
D58V3, multiclass
                                                                                          clus
vv                                                                                         15Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         15Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 10
  REGIONAL LYMPH NODE                                                                                      44
D58V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4    2
  15Q LOSS WILD-TYPE   18   43
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                4                 18
  MALE                  2                 43
                    vv
clus                 M0 M1 M1A M1B M1C
  15Q LOSS MUTATED    5  0   0   1   0
  15Q LOSS WILD-TYPE 51  1   1   0   2
D58V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  15Q LOSS MUTATED    4  0   0   0   0   0   1  1  0
  15Q LOSS WILD-TYPE 29  1   2   7   1   5   2  6  2
D58V6, multiclass
D58V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  15Q LOSS MUTATED             0       1        0        1        1         0
  15Q LOSS WILD-TYPE           2       9        2        4        7         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  15Q LOSS MUTATED           1         1          0          0          0
  15Q LOSS WILD-TYPE         1         4          2          7          9
                    vv
clus                 STAGE IV
  15Q LOSS MUTATED          0
  15Q LOSS WILD-TYPE        3
D58V8, multiclass

Clustering(59) Variable = 16p loss mutation analysis
D59V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    2  3
  16P LOSS WILD-TYPE 30 31
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                 61 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 31 
$`16P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EE-A2MK TCGA-GN-A262 
      112.54        36.03       176.55       144.76       120.46 

$`16P LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       71.80       121.22        31.59        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HY 
       58.03        60.23         9.30       148.31         6.38       117.17 
TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       20.38        35.93       107.34        61.18        53.92       215.44 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       15.68        26.86       109.64        78.87       168.26        63.32 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
       47.84        39.62        32.19        44.35        56.42       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT 
       58.75        47.54       135.91       182.01        55.59        19.56 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67       129.24        28.80        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
       16.96       248.61       122.73         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC 
      138.77         6.41        48.59       228.59         7.76       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
       53.52        15.45        32.71       101.26        11.41       148.77 
TCGA-GN-A265 
       84.72 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             36.03               3.68 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            176.55             357.37 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            120.46              53.92 
[1] "36.0 - 176.6 (120.5)" "3.7 - 357.4 (53.9)"  
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D59V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16P LOSS MUTATED                    0             0
  16P LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16P LOSS MUTATED                                                                                          1
  16P LOSS WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  16P LOSS MUTATED                     4
  16P LOSS WILD-TYPE                  44
D59V3, multiclass
                                                                                          clus
vv                                                                                         16P LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         16P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      44
D59V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    2
  16P LOSS WILD-TYPE   19   43
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                 19
  MALE                  2                 43
                    vv
clus                 M0 M1 M1A M1B M1C
  16P LOSS MUTATED    4  0   0   0   0
  16P LOSS WILD-TYPE 52  1   1   1   2
D59V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  16P LOSS MUTATED    2  0   0   1   0   1   0  0  0
  16P LOSS WILD-TYPE 31  1   2   6   1   4   3  7  2
D59V6, multiclass
D59V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16P LOSS MUTATED             1       0        0        0        1         0
  16P LOSS WILD-TYPE           1      10        2        5        7         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  16P LOSS MUTATED           0         0          0          1          1
  16P LOSS WILD-TYPE         2         5          2          6          8
                    vv
clus                 STAGE IV
  16P LOSS MUTATED          0
  16P LOSS WILD-TYPE        3
D59V8, multiclass

Clustering(60) Variable = 16q loss mutation analysis
D60V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    4  6
  16Q LOSS WILD-TYPE 28 28
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                 56 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                 28 
$`16Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D9-A148 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F8 
      112.54       148.31        36.03       176.55        35.93        15.68 
TCGA-EE-A2MK TCGA-EE-A3AF TCGA-FS-A1ZF TCGA-GN-A262 
      144.76        13.81        15.45       120.46 

$`16Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       71.80       121.22        31.59        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I0 
       58.03        60.23         9.30         6.38       117.17        20.38 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A183 TCGA-EE-A20B 
      107.34        61.18        53.92       215.44        26.86       109.64 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       78.87       168.26        63.32        47.84        39.62        32.19 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       44.35        56.42       345.96        58.75        47.54       135.91 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
      182.01        55.59        19.56        21.67       129.24        28.80 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A3AB 
       19.76       103.27       103.17        16.96       248.61       122.73 
TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY 
        3.68        23.47       138.77         6.41        48.59       228.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR 
        7.76       357.37        53.52        32.71       101.26        11.41 
TCGA-FS-A1ZS TCGA-GN-A265 
      148.77        84.72 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             13.81               3.68 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            176.55             357.37 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            74.285             56.005 
[1] "13.8 - 176.6 (74.3)" "3.7 - 357.4 (56.0)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D60V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16Q LOSS MUTATED                    1             0
  16Q LOSS WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16Q LOSS MUTATED                                                                                          2
  16Q LOSS WILD-TYPE                                                                                       10
                    vv
clus                 REGIONAL LYMPH NODE
  16Q LOSS MUTATED                     7
  16Q LOSS WILD-TYPE                  41
D60V3, multiclass
                                                                                          clus
vv                                                                                         16Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         16Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 10
  REGIONAL LYMPH NODE                                                                                      41
D60V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5    5
  16Q LOSS WILD-TYPE   17   40
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                5                 17
  MALE                  5                 40
                    vv
clus                 M0 M1 M1A M1B M1C
  16Q LOSS MUTATED    7  0   0   1   0
  16Q LOSS WILD-TYPE 49  1   1   0   2
D60V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  16Q LOSS MUTATED    3  0   0   1   0   3   0  1  0
  16Q LOSS WILD-TYPE 30  1   2   6   1   2   3  6  2
D60V6, multiclass
D60V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16Q LOSS MUTATED             1       0        0        0        1         0
  16Q LOSS WILD-TYPE           1      10        2        5        7         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  16Q LOSS MUTATED           1         0          0          3          1
  16Q LOSS WILD-TYPE         1         5          2          4          8
                    vv
clus                 STAGE IV
  16Q LOSS MUTATED          0
  16Q LOSS WILD-TYPE        3
D60V8, multiclass

Clustering(61) Variable = 17p loss mutation analysis
D61V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED    8  4
  17P LOSS WILD-TYPE 24 30
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                12                 54 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 4                 30 
$`17P LOSS MUTATED`
TCGA-D3-A3MO TCGA-D9-A148 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-EE-A29C TCGA-EE-A29H 
        9.30       148.31        36.03       117.17        47.84        32.19 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-FS-A1YX TCGA-FS-A1ZH 
       44.35       345.96        19.56       129.24        48.59        32.71 

$`17P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D9-A1JX TCGA-DA-A1I0 TCGA-DA-A1I2 
       12.10        58.03        60.23         6.38        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
       35.93       107.34        61.18        53.92       215.44        15.68 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E 
       26.86       109.64        78.87       168.26        63.32        39.62 
TCGA-EE-A29P TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS 
       56.42        58.75        47.54       135.91       182.01        55.59 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       21.67        28.80        19.76       103.27       103.17        16.96 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      144.76       248.61       122.73         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      138.77         6.41       228.59         7.76       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       15.45       101.26        11.41       148.77       120.46        84.72 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              9.30               3.68 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            345.96             357.37 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            46.095             58.390 
[1] "9.3 - 346.0 (46.1)" "3.7 - 357.4 (58.4)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D61V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17P LOSS MUTATED                    0             1
  17P LOSS WILD-TYPE                  6             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17P LOSS MUTATED                                                                                          2
  17P LOSS WILD-TYPE                                                                                       10
                    vv
clus                 REGIONAL LYMPH NODE
  17P LOSS MUTATED                     9
  17P LOSS WILD-TYPE                  39
D61V3, multiclass
                                                                                          clus
vv                                                                                         17P LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     9
                                                                                          clus
vv                                                                                         17P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 10
  REGIONAL LYMPH NODE                                                                                      39
D61V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6    6
  17P LOSS WILD-TYPE   16   39
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                6                 16
  MALE                  6                 39
                    vv
clus                 M0 M1 M1A M1B M1C
  17P LOSS MUTATED   10  0   0   1   1
  17P LOSS WILD-TYPE 46  1   1   0   1
D61V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  17P LOSS MUTATED    6  0   0   1   0   0   2  2  1
  17P LOSS WILD-TYPE 27  1   2   6   1   5   1  5  1
D61V6, multiclass
D61V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17P LOSS MUTATED             0       2        1        2        0         1
  17P LOSS WILD-TYPE           2       8        1        3        8         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  17P LOSS MUTATED           0         1          0          1          1
  17P LOSS WILD-TYPE         2         4          2          6          8
                    vv
clus                 STAGE IV
  17P LOSS MUTATED          1
  17P LOSS WILD-TYPE        2
D61V8, multiclass

Clustering(62) Variable = 17q loss mutation analysis
D62V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    3  2
  17Q LOSS WILD-TYPE 29 32
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 61 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 32 
$`17Q LOSS MUTATED`
TCGA-DA-A1HW TCGA-EE-A29C TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-FS-A1ZH 
       36.03        47.84        19.56       129.24        32.71 

$`17Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX 
       12.10        58.03        60.23         9.30       148.31         6.38 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.17        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       53.92       215.44        15.68        26.86       109.64        78.87 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
      168.26        63.32        39.62        32.19        44.35        56.42 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS 
      345.96        58.75        47.54       135.91       182.01        55.59 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       21.67        28.80        19.76       103.27       103.17        16.96 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      144.76       248.61       122.73         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC 
      138.77         6.41        48.59       228.59         7.76       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
       53.52        15.45       101.26        11.41       148.77       120.46 
TCGA-GN-A265 
       84.72 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             19.56               3.68 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            129.24             357.37 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             36.03              58.03 
[1] "19.6 - 129.2 (36.0)" "3.7 - 357.4 (58.0)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D62V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17Q LOSS MUTATED                    0             0
  17Q LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17Q LOSS MUTATED                                                                                          0
  17Q LOSS WILD-TYPE                                                                                       12
                    vv
clus                 REGIONAL LYMPH NODE
  17Q LOSS MUTATED                     5
  17Q LOSS WILD-TYPE                  43
D62V3, multiclass
                                                                                          clus
vv                                                                                         17Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         17Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 12
  REGIONAL LYMPH NODE                                                                                      43
D62V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    3
  17Q LOSS WILD-TYPE   20   42
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                2                 20
  MALE                  3                 42
                    vv
clus                 M0 M1 M1A M1B M1C
  17Q LOSS MUTATED    4  0   0   0   1
  17Q LOSS WILD-TYPE 52  1   1   1   1
D62V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  17Q LOSS MUTATED    3  0   0   1   0   0   1  0  0
  17Q LOSS WILD-TYPE 30  1   2   6   1   5   2  7  2
D62V6, multiclass
D62V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17Q LOSS MUTATED             0       1        0        1        0         1
  17Q LOSS WILD-TYPE           2       9        2        4        8         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  17Q LOSS MUTATED           0         0          0          1          0
  17Q LOSS WILD-TYPE         2         5          2          6          9
                    vv
clus                 STAGE IV
  17Q LOSS MUTATED          1
  17Q LOSS WILD-TYPE        2
D62V8, multiclass

Clustering(63) Variable = 18p loss mutation analysis
D63V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   10  6
  18P LOSS WILD-TYPE 22 28
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                16                 50 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 6                 28 
$`18P LOSS MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3C6 TCGA-D9-A1JX TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 
       71.80        58.03         6.38       176.55        61.18       215.44 
TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2MK TCGA-EE-A3AG 
      109.64        63.32        44.35       345.96       144.76        23.47 
TCGA-EE-A3AH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
      138.77       101.26        11.41       148.77 

$`18P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
      112.54       121.22        31.59        23.77        11.87        12.10 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       60.23         9.30       148.31        36.03       117.17        20.38 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F 
       35.93       107.34        53.92        15.68        26.86        78.87 
TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2A6 
      168.26        47.84        39.62        32.19        56.42        58.75 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       47.54       135.91       182.01        55.59        19.56        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
      129.24        28.80        19.76       103.27       103.17        16.96 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-ER-A19J TCGA-FS-A1YX 
      248.61       122.73         3.68        13.81         6.41        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
      228.59         7.76       357.37        53.52        15.45        32.71 
TCGA-GN-A262 TCGA-GN-A265 
      120.46        84.72 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              6.38               3.68 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            345.96             357.37 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            86.530             48.215 
[1] "6.4 - 346.0 (86.5)" "3.7 - 357.4 (48.2)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "2"  
D63V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18P LOSS MUTATED                    1             1
  18P LOSS WILD-TYPE                  5             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18P LOSS MUTATED                                                                                          6
  18P LOSS WILD-TYPE                                                                                        6
                    vv
clus                 REGIONAL LYMPH NODE
  18P LOSS MUTATED                     8
  18P LOSS WILD-TYPE                  40
D63V3, multiclass
                                                                                          clus
vv                                                                                         18P LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                     8
                                                                                          clus
vv                                                                                         18P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  6
  REGIONAL LYMPH NODE                                                                                      40
D63V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      6   10
  18P LOSS WILD-TYPE   16   35
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                6                 16
  MALE                 10                 35
                    vv
clus                 M0 M1 M1A M1B M1C
  18P LOSS MUTATED   15  0   0   0   0
  18P LOSS WILD-TYPE 41  1   1   1   2
D63V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  18P LOSS MUTATED    7  0   1   1   0   2   1  1  2
  18P LOSS WILD-TYPE 26  1   1   6   1   3   2  6  0
D63V6, multiclass
D63V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18P LOSS MUTATED             0       0        0        2        5         0
  18P LOSS WILD-TYPE           2      10        2        3        3         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  18P LOSS MUTATED           0         2          1          1          2
  18P LOSS WILD-TYPE         2         3          1          6          7
                    vv
clus                 STAGE IV
  18P LOSS MUTATED          0
  18P LOSS WILD-TYPE        3
D63V8, multiclass

Clustering(64) Variable = 18q loss mutation analysis
D64V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   10  7
  18Q LOSS WILD-TYPE 22 27
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                17                 49 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 7                 27 
$`18Q LOSS MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D9-A148 TCGA-DA-A1I2 
       71.80        31.59        58.03        60.23       148.31       176.55 
TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29M TCGA-EE-A29P 
       61.18       215.44       109.64        63.32        44.35        56.42 
TCGA-EE-A29T TCGA-EE-A2MK TCGA-EE-A3AH TCGA-FS-A1ZM TCGA-FS-A1ZS 
      345.96       144.76       138.77       101.26       148.77 

$`18Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3MO 
      112.54       121.22        23.77        11.87        12.10         9.30 
TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 
        6.38        36.03       117.17        20.38        35.93       107.34 
TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29C 
       53.92        15.68        26.86        78.87       168.26        47.84 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
       39.62        32.19        58.75        47.54       135.91       182.01 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
       55.59        19.56        21.67       129.24        28.80        19.76 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD 
      103.27       103.17        16.96       248.61       122.73         3.68 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
       13.81        23.47         6.41        48.59       228.59         7.76 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZR TCGA-GN-A262 
      357.37        53.52        15.45        32.71        11.41       120.46 
TCGA-GN-A265 
       84.72 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             31.59               3.68 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            345.96             357.37 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            101.26              39.62 
[1] "31.6 - 346.0 (101.3)" "3.7 - 357.4 (39.6)"  
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "2.1"
D64V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18Q LOSS MUTATED                    1             1
  18Q LOSS WILD-TYPE                  5             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18Q LOSS MUTATED                                                                                          4
  18Q LOSS WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  18Q LOSS MUTATED                    11
  18Q LOSS WILD-TYPE                  37
D64V3, multiclass
                                                                                          clus
vv                                                                                         18Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                    11
                                                                                          clus
vv                                                                                         18Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      37
D64V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      7   10
  18Q LOSS WILD-TYPE   15   35
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                7                 15
  MALE                 10                 35
                    vv
clus                 M0 M1 M1A M1B M1C
  18Q LOSS MUTATED   16  0   0   1   0
  18Q LOSS WILD-TYPE 40  1   1   0   2
D64V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  18Q LOSS MUTATED    7  0   1   2   1   2   1  2  1
  18Q LOSS WILD-TYPE 26  1   1   5   0   3   2  5  1
D64V6, multiclass
D64V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18Q LOSS MUTATED             0       0        0        2        4         0
  18Q LOSS WILD-TYPE           2      10        2        3        4         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  18Q LOSS MUTATED           1         3          1          2          2
  18Q LOSS WILD-TYPE         1         2          1          5          7
                    vv
clus                 STAGE IV
  18Q LOSS MUTATED          0
  18Q LOSS WILD-TYPE        3
D64V8, multiclass

Clustering(65) Variable = 19p loss mutation analysis
D65V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    2  4
  19P LOSS WILD-TYPE 30 30
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 6                 60 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 30 
$`19P LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D9-A148 TCGA-DA-A1HW TCGA-DA-A1I8 TCGA-EE-A29H TCGA-FS-A1ZH 
       31.59       148.31        36.03        53.92        32.19        32.71 

$`19P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
      112.54        71.80       121.22        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I0 
       58.03        60.23         9.30         6.38       117.17        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 
      176.55        35.93       107.34        61.18       215.44        15.68 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       26.86       109.64        78.87       168.26        63.32        47.84 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB 
       39.62        44.35        56.42       345.96        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
      135.91       182.01        55.59        19.56        21.67       129.24 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.80        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      248.61       122.73         3.68        13.81        23.47       138.77 
TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
        6.41        48.59       228.59         7.76       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       15.45       101.26        11.41       148.77       120.46        84.72 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             31.59               3.68 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            148.31             357.37 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             34.37              58.39 
[1] "31.6 - 148.3 (34.4)" "3.7 - 357.4 (58.4)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D65V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19P LOSS MUTATED                    0             0
  19P LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19P LOSS MUTATED                                                                                          1
  19P LOSS WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  19P LOSS MUTATED                     5
  19P LOSS WILD-TYPE                  43
D65V3, multiclass
                                                                                          clus
vv                                                                                         19P LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         19P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      43
D65V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4    2
  19P LOSS WILD-TYPE   18   43
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                4                 18
  MALE                  2                 43
                    vv
clus                 M0 M1 M1A M1B M1C
  19P LOSS MUTATED    4  0   0   1   1
  19P LOSS WILD-TYPE 52  1   1   0   1
D65V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  19P LOSS MUTATED    1  0   0   1   1   0   1  2  0
  19P LOSS WILD-TYPE 32  1   2   6   0   5   2  5  2
D65V6, multiclass
D65V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19P LOSS MUTATED             0       0        1        0        0         0
  19P LOSS WILD-TYPE           2      10        1        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  19P LOSS MUTATED           0         0          0          2          1
  19P LOSS WILD-TYPE         2         5          2          5          8
                    vv
clus                 STAGE IV
  19P LOSS MUTATED          1
  19P LOSS WILD-TYPE        2
D65V8, multiclass

Clustering(66) Variable = 19q loss mutation analysis
D66V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    5  3
  19Q LOSS WILD-TYPE 27 31
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 8                 58 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 31 
$`19Q LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D9-A148 TCGA-DA-A1I8 TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A3AD 
       31.59       148.31        53.92        32.19        44.35         3.68 
TCGA-EE-A3AG TCGA-FS-A1ZH 
       23.47        32.71 

$`19Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
      112.54        71.80       121.22        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY 
       58.03        60.23         9.30         6.38        36.03       117.17 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 
       20.38       176.55        35.93       107.34        61.18       215.44 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       15.68        26.86       109.64        78.87       168.26        63.32 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB 
       47.84        39.62        56.42       345.96        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
      135.91       182.01        55.59        19.56        21.67       129.24 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.80        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AF TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX 
      248.61       122.73        13.81       138.77         6.41        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZM 
      228.59         7.76       357.37        53.52        15.45       101.26 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       11.41       148.77       120.46        84.72 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              3.68               6.38 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            148.31             357.37 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             32.45              59.49 
[1] "3.7 - 148.3 (32.5)" "6.4 - 357.4 (59.5)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19Q LOSS MUTATED                    0             1
  19Q LOSS WILD-TYPE                  6             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19Q LOSS MUTATED                                                                                          2
  19Q LOSS WILD-TYPE                                                                                       10
                    vv
clus                 REGIONAL LYMPH NODE
  19Q LOSS MUTATED                     5
  19Q LOSS WILD-TYPE                  43
D66V3, multiclass
                                                                                          clus
vv                                                                                         19Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         19Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 10
  REGIONAL LYMPH NODE                                                                                      43
D66V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4    4
  19Q LOSS WILD-TYPE   18   41
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                4                 18
  MALE                  4                 41
                    vv
clus                 M0 M1 M1A M1B M1C
  19Q LOSS MUTATED    4  0   0   1   1
  19Q LOSS WILD-TYPE 52  1   1   0   1
D66V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  19Q LOSS MUTATED    2  0   0   0   1   0   1  2  0
  19Q LOSS WILD-TYPE 31  1   2   7   0   5   2  5  2
D66V6, multiclass
D66V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19Q LOSS MUTATED             0       0        1        1        0         0
  19Q LOSS WILD-TYPE           2      10        1        4        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  19Q LOSS MUTATED           0         0          0          1          1
  19Q LOSS WILD-TYPE         2         5          2          6          8
                    vv
clus                 STAGE IV
  19Q LOSS MUTATED          1
  19Q LOSS WILD-TYPE        2
D66V8, multiclass

Clustering(67) Variable = 20p loss mutation analysis
D67V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    2  1
  20P LOSS WILD-TYPE 30 33
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 63 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 33 
$`20P LOSS MUTATED`
TCGA-EE-A29E TCGA-EE-A29P TCGA-FS-A1ZR 
       39.62        56.42        11.41 

$`20P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX 
       12.10        58.03        60.23         9.30       148.31         6.38 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       36.03       117.17        20.38       176.55        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
       61.18        53.92       215.44        15.68        26.86       109.64 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
       78.87       168.26        63.32        47.84        32.19        44.35 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS 
      345.96        58.75        47.54       135.91       182.01        55.59 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME 
       19.56        21.67       129.24        28.80        19.76       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD 
      103.17        16.96       144.76       248.61       122.73         3.68 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY 
       13.81        23.47       138.77         6.41        48.59       228.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM 
        7.76       357.37        53.52        15.45        32.71       101.26 
TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
      148.77       120.46        84.72 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             11.41               3.68 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             56.42             357.37 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             39.62              58.03 
[1] "11.4 - 56.4 (39.6)" "3.7 - 357.4 (58.0)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D67V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20P LOSS MUTATED                    0             0
  20P LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20P LOSS MUTATED                                                                                          1
  20P LOSS WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  20P LOSS MUTATED                     2
  20P LOSS WILD-TYPE                  46
D67V3, multiclass
                                                                                          clus
vv                                                                                         20P LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         20P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      46
D67V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    2
  20P LOSS WILD-TYPE   21   43
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                1                 21
  MALE                  2                 43
                    vv
clus                 M0 M1 M1A M1B M1C
  20P LOSS MUTATED    3  0   0   0   0
  20P LOSS WILD-TYPE 53  1   1   1   2
D67V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  20P LOSS MUTATED    2  0   0   1   0   0   0  0  0
  20P LOSS WILD-TYPE 31  1   2   6   1   5   3  7  2
D67V6, multiclass
D67V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  20P LOSS MUTATED             0       0        0        0        1         0
  20P LOSS WILD-TYPE           2      10        2        5        7         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  20P LOSS MUTATED           1         0          0          1          0
  20P LOSS WILD-TYPE         1         5          2          6          9
                    vv
clus                 STAGE IV
  20P LOSS MUTATED          0
  20P LOSS WILD-TYPE        3
D67V8, multiclass

Clustering(68) Variable = 21q loss mutation analysis
D68V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    5  3
  21Q LOSS WILD-TYPE 27 31
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                 58 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 31 
$`21Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-EE-A20B TCGA-EE-A29H TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2M5 
      112.54       109.64        32.19        58.75        47.54        21.67 
TCGA-EE-A2MK TCGA-EE-A3AH 
      144.76       138.77 

$`21Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       71.80       121.22        31.59        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       58.03        60.23         9.30       148.31         6.38        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.17        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A20H 
       53.92       215.44        15.68        26.86        78.87       168.26 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
       63.32        47.84        39.62        44.35        56.42       345.96 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2M7 
      135.91       182.01        55.59        19.56       129.24        28.80 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A3AB 
       19.76       103.27       103.17        16.96       248.61       122.73 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY 
        3.68        13.81        23.47         6.41        48.59       228.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM 
        7.76       357.37        53.52        15.45        32.71       101.26 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       11.41       148.77       120.46        84.72 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             21.67               3.68 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            144.76             357.37 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            84.195             54.755 
[1] "21.7 - 144.8 (84.2)" "3.7 - 357.4 (54.8)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D68V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  21Q LOSS MUTATED                    0             0
  21Q LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  21Q LOSS MUTATED                                                                                          1
  21Q LOSS WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  21Q LOSS MUTATED                     7
  21Q LOSS WILD-TYPE                  41
D68V3, multiclass
                                                                                          clus
vv                                                                                         21Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         21Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      41
D68V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    5
  21Q LOSS WILD-TYPE   19   40
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                3                 19
  MALE                  5                 40
                    vv
clus                 M0 M1 M1A M1B M1C
  21Q LOSS MUTATED    8  0   0   0   0
  21Q LOSS WILD-TYPE 48  1   1   1   2
D68V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  21Q LOSS MUTATED    7  0   1   0   0   0   0  0  0
  21Q LOSS WILD-TYPE 26  1   1   7   1   5   3  7  2
D68V6, multiclass
D68V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  21Q LOSS MUTATED             1       1        2        0        3         0
  21Q LOSS WILD-TYPE           1       9        0        5        5         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  21Q LOSS MUTATED           0         0          1          0          0
  21Q LOSS WILD-TYPE         2         5          1          7          9
                    vv
clus                 STAGE IV
  21Q LOSS MUTATED          0
  21Q LOSS WILD-TYPE        3
D68V8, multiclass

Clustering(69) Variable = 22q loss mutation analysis
D69V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    2  2
  22Q LOSS WILD-TYPE 30 32
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 4                 62 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 2                 32 
$`22Q LOSS MUTATED`
TCGA-DA-A1I2 TCGA-EE-A29C TCGA-EE-A2A6 TCGA-FS-A1YX 
      176.55        47.84        58.75        48.59 

$`22Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX 
       12.10        58.03        60.23         9.30       148.31         6.38 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       36.03       117.17        20.38        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       53.92       215.44        15.68        26.86       109.64        78.87 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
      168.26        63.32        39.62        32.19        44.35        56.42 
TCGA-EE-A29T TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT 
      345.96        47.54       135.91       182.01        55.59        19.56 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67       129.24        28.80        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF 
       16.96       144.76       248.61       122.73         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC 
       23.47       138.77         6.41       228.59         7.76       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
       53.52        15.45        32.71       101.26        11.41       148.77 
TCGA-GN-A262 TCGA-GN-A265 
      120.46        84.72 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             47.84               3.68 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            176.55             357.37 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            53.670             56.005 
[1] "47.8 - 176.6 (53.7)" "3.7 - 357.4 (56.0)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D9-A148         TCGA-D9-A1JX 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GB         TCGA-EE-A2GE 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GS         TCGA-EE-A2GT 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2ME         TCGA-EE-A2MG 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2MH         TCGA-EE-A2MK         TCGA-EE-A2MP 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A3AB         TCGA-EE-A3AD         TCGA-EE-A3AF 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A3AG         TCGA-EE-A3AH         TCGA-ER-A19J 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1YX         TCGA-FS-A1YY         TCGA-FS-A1Z7 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZC         TCGA-FS-A1ZD         TCGA-FS-A1ZF 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZH         TCGA-FS-A1ZM         TCGA-FS-A1ZR 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZS         TCGA-GN-A262         TCGA-GN-A265 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D69V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  22Q LOSS MUTATED                    0             0
  22Q LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  22Q LOSS MUTATED                                                                                          1
  22Q LOSS WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  22Q LOSS MUTATED                     3
  22Q LOSS WILD-TYPE                  45
D69V3, multiclass
                                                                                          clus
vv                                                                                         22Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         22Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      45
D69V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1    3
  22Q LOSS WILD-TYPE   21   42
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                1                 21
  MALE                  3                 42
                    vv
clus                 M0 M1 M1A M1B M1C
  22Q LOSS MUTATED    4  0   0   0   0
  22Q LOSS WILD-TYPE 52  1   1   1   2
D69V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  22Q LOSS MUTATED    3  0   0   0   0   1   0  0  0
  22Q LOSS WILD-TYPE 30  1   2   7   1   4   3  7  2
D69V6, multiclass
D69V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  22Q LOSS MUTATED             0       1        1        1        0         0
  22Q LOSS WILD-TYPE           2       9        1        4        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  22Q LOSS MUTATED           0         0          0          0          1
  22Q LOSS WILD-TYPE         2         5          2          7          8
                    vv
clus                 STAGE IV
  22Q LOSS MUTATED          0
  22Q LOSS WILD-TYPE        3
D69V8, multiclass

Clustering(70) Variable = Xq loss mutation analysis
D70V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    2  2
  XQ LOSS WILD-TYPE 30 32
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                62 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                32 
$`XQ LOSS MUTATED`
TCGA-D3-A3C6 TCGA-EE-A29H TCGA-FS-A1ZC TCGA-GN-A262 
       58.03        32.19       357.37       120.46 

$`XQ LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       12.10        60.23         9.30       148.31         6.38        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
      117.17        20.38       176.55        35.93       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       53.92       215.44        15.68        26.86       109.64        78.87 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P 
      168.26        63.32        47.84        39.62        44.35        56.42 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS 
      345.96        58.75        47.54       135.91       182.01        55.59 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME 
       19.56        21.67       129.24        28.80        19.76       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD 
      103.17        16.96       144.76       248.61       122.73         3.68 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY 
       13.81        23.47       138.77         6.41        48.59       228.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR 
        7.76        53.52        15.45        32.71       101.26        11.41 
TCGA-FS-A1ZS TCGA-GN-A265 
      148.77        84.72 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            32.19              3.68 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           357.37            345.96 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           89.245            54.755 
[1] "32.2 - 357.4 (89.2)" "3.7 - 346.0 (54.8)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-D9-A148        TCGA-D9-A1JX 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AD        TCGA-EE-A3AF        TCGA-EE-A3AG 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19J        TCGA-FS-A1YX        TCGA-FS-A1YY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
[1] "hr=" "3"  
D70V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  XQ LOSS MUTATED                    1             0
  XQ LOSS WILD-TYPE                  5             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  XQ LOSS MUTATED                                                                                          1
  XQ LOSS WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  XQ LOSS MUTATED                     2
  XQ LOSS WILD-TYPE                  46
D70V3, multiclass
                                                                                          clus
vv                                                                                         XQ LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         XQ LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     46
D70V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    1
  XQ LOSS WILD-TYPE   19   44
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               3                19
  MALE                 1                44
                   vv
clus                M0 M1 M1A M1B M1C
  XQ LOSS MUTATED    3  0   0   0   0
  XQ LOSS WILD-TYPE 53  1   1   1   2
D70V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  XQ LOSS MUTATED    3  0   0   0   0   0   0  0  0
  XQ LOSS WILD-TYPE 30  1   2   7   1   5   3  7  2
D70V6, multiclass
D70V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  XQ LOSS MUTATED             1       0        1        1        0         0
  XQ LOSS WILD-TYPE           1      10        1        4        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XQ LOSS MUTATED           0         0          0          0          0
  XQ LOSS WILD-TYPE         2         5          2          7          9
                   vv
clus                STAGE IV
  XQ LOSS MUTATED          0
  XQ LOSS WILD-TYPE        3
D70V8, multiclass
                     V1.D                        V2                        V3 
          "Time to Death"                     "AGE" "PRIMARY.SITE.OF.DISEASE" 
                       V4                        V5                        V6 
                 "GENDER"      "DISTANT.METASTASIS"   "LYMPH.NODE.METASTASIS" 
                       V7                        V8 
        "TUMOR.STAGECODE"   "NEOPLASM.DISEASESTAGE" 
> q(save="no")
