
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/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.81.4078/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.81.4078/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/404281/SKCM-NF1_Any_Mutants.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-NF1_Any_Mutants/3215661/SKCM-NF1_Any_Mutants.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=", "-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="
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=25, in cluster file=31, common to both=25
[1] "Reduce the number of clustering variables from 76 to 74."
[1] 74 25
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             8             17 
  NRAS MUTATED NRAS WILD-TYPE 
             8             17 
[1] "TPTE MUTATION ANALYSIS"
[1] 3
  TPTE MUTATED TPTE WILD-TYPE 
            14             11 
  TPTE MUTATED TPTE WILD-TYPE 
            14             11 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             7             18 
  TP53 MUTATED TP53 WILD-TYPE 
             7             18 
[1] "GRXCR1 MUTATION ANALYSIS"
[1] 3
  GRXCR1 MUTATED GRXCR1 WILD-TYPE 
               7               18 
  GRXCR1 MUTATED GRXCR1 WILD-TYPE 
               7               18 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
             7             18 
  BRAF MUTATED BRAF WILD-TYPE 
             7             18 
[1] "TRAT1 MUTATION ANALYSIS"
[1] 3
  TRAT1 MUTATED TRAT1 WILD-TYPE 
              7              18 
  TRAT1 MUTATED TRAT1 WILD-TYPE 
              7              18 
[1] "ZNF585B MUTATION ANALYSIS"
[1] 3
  ZNF585B MUTATED ZNF585B WILD-TYPE 
                8                17 
  ZNF585B MUTATED ZNF585B WILD-TYPE 
                8                17 
[1] "TPTE2 MUTATION ANALYSIS"
[1] 3
  TPTE2 MUTATED TPTE2 WILD-TYPE 
             11              14 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
             11              14 
[1] "OR51S1 MUTATION ANALYSIS"
[1] 3
  OR51S1 MUTATED OR51S1 WILD-TYPE 
               8               17 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
               8               17 
[1] "RAC1 MUTATION ANALYSIS"
[1] 3
  RAC1 MUTATED RAC1 WILD-TYPE 
             4             21 
  RAC1 MUTATED RAC1 WILD-TYPE 
             4             21 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               5               20 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               5               20 
[1] "C7 MUTATION ANALYSIS"
[1] 3
  C7 MUTATED C7 WILD-TYPE 
          11           14 
  C7 MUTATED C7 WILD-TYPE 
          11           14 
[1] "C15ORF23 MUTATION ANALYSIS"
[1] 3
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                 5                 20 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                 5                 20 
[1] "GLRB MUTATION ANALYSIS"
[1] 3
  GLRB MUTATED GLRB WILD-TYPE 
             6             19 
  GLRB MUTATED GLRB WILD-TYPE 
             6             19 
[1] "FAM58A MUTATION ANALYSIS"
[1] 3
  FAM58A MUTATED FAM58A WILD-TYPE 
               3               22 
  FAM58A MUTATED FAM58A WILD-TYPE 
               3               22 
[1] "EPHA6 MUTATION ANALYSIS"
[1] 3
  EPHA6 MUTATED EPHA6 WILD-TYPE 
             11              14 
  EPHA6 MUTATED EPHA6 WILD-TYPE 
             11              14 
[1] "NAP1L2 MUTATION ANALYSIS"
[1] 3
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               7               18 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               7               18 
[1] "OR4K5 MUTATION ANALYSIS"
[1] 3
  OR4K5 MUTATED OR4K5 WILD-TYPE 
              8              17 
  OR4K5 MUTATED OR4K5 WILD-TYPE 
              8              17 
[1] "SLC9A11 MUTATION ANALYSIS"
[1] 3
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
               11                14 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
               11                14 
[1] "ADAMTS20 MUTATION ANALYSIS"
[1] 3
  ADAMTS20 MUTATED ADAMTS20 WILD-TYPE 
                15                 10 
  ADAMTS20 MUTATED ADAMTS20 WILD-TYPE 
                15                 10 
[1] "SLC38A4 MUTATION ANALYSIS"
[1] 3
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
                9                16 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
                9                16 
[1] "OR2T2 MUTATION ANALYSIS"
[1] 3
  OR2T2 MUTATED OR2T2 WILD-TYPE 
              5              20 
  OR2T2 MUTATED OR2T2 WILD-TYPE 
              5              20 
[1] "PRB2 MUTATION ANALYSIS"
[1] 3
  PRB2 MUTATED PRB2 WILD-TYPE 
             9             16 
  PRB2 MUTATED PRB2 WILD-TYPE 
             9             16 
[1] "COL21A1 MUTATION ANALYSIS"
[1] 3
  COL21A1 MUTATED COL21A1 WILD-TYPE 
               10                15 
  COL21A1 MUTATED COL21A1 WILD-TYPE 
               10                15 
[1] "OR4N2 MUTATION ANALYSIS"
[1] 3
  OR4N2 MUTATED OR4N2 WILD-TYPE 
              9              16 
  OR4N2 MUTATED OR4N2 WILD-TYPE 
              9              16 
[1] "PROX1 MUTATION ANALYSIS"
[1] 3
  PROX1 MUTATED PROX1 WILD-TYPE 
              6              19 
  PROX1 MUTATED PROX1 WILD-TYPE 
              6              19 
[1] "ANGPT1 MUTATION ANALYSIS"
[1] 3
  ANGPT1 MUTATED ANGPT1 WILD-TYPE 
               9               16 
  ANGPT1 MUTATED ANGPT1 WILD-TYPE 
               9               16 
[1] "C8A MUTATION ANALYSIS"
[1] 3
  C8A MUTATED C8A WILD-TYPE 
            8            17 
  C8A MUTATED C8A WILD-TYPE 
            8            17 
[1] "SERPINB11 MUTATION ANALYSIS"
[1] 3
  SERPINB11 MUTATED SERPINB11 WILD-TYPE 
                  7                  18 
  SERPINB11 MUTATED SERPINB11 WILD-TYPE 
                  7                  18 
[1] "C18ORF34 MUTATION ANALYSIS"
[1] 3
  C18ORF34 MUTATED C18ORF34 WILD-TYPE 
                10                 15 
  C18ORF34 MUTATED C18ORF34 WILD-TYPE 
                10                 15 
[1] "FRG2B MUTATION ANALYSIS"
[1] 3
  FRG2B MUTATED FRG2B WILD-TYPE 
              5              20 
  FRG2B MUTATED FRG2B WILD-TYPE 
              5              20 
[1] "LPPR1 MUTATION ANALYSIS"
[1] 3
  LPPR1 MUTATED LPPR1 WILD-TYPE 
              4              21 
  LPPR1 MUTATED LPPR1 WILD-TYPE 
              4              21 
[1] "THEMIS MUTATION ANALYSIS"
[1] 3
  THEMIS MUTATED THEMIS WILD-TYPE 
               7               18 
  THEMIS MUTATED THEMIS WILD-TYPE 
               7               18 
[1] "SNAP91 MUTATION ANALYSIS"
[1] 3
  SNAP91 MUTATED SNAP91 WILD-TYPE 
               7               18 
  SNAP91 MUTATED SNAP91 WILD-TYPE 
               7               18 
[1] "SLC27A6 MUTATION ANALYSIS"
[1] 3
  SLC27A6 MUTATED SLC27A6 WILD-TYPE 
                8                17 
  SLC27A6 MUTATED SLC27A6 WILD-TYPE 
                8                17 
[1] "CXORF22 MUTATION ANALYSIS"
[1] 3
  CXORF22 MUTATED CXORF22 WILD-TYPE 
                8                17 
  CXORF22 MUTATED CXORF22 WILD-TYPE 
                8                17 
[1] "NOBOX MUTATION ANALYSIS"
[1] 3
  NOBOX MUTATED NOBOX WILD-TYPE 
              8              17 
  NOBOX MUTATED NOBOX WILD-TYPE 
              8              17 
[1] "MUC7 MUTATION ANALYSIS"
[1] 3
  MUC7 MUTATED MUC7 WILD-TYPE 
             5             20 
  MUC7 MUTATED MUC7 WILD-TYPE 
             5             20 
[1] "GIMAP7 MUTATION ANALYSIS"
[1] 3
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
               5               20 
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
               5               20 
[1] "SYT17 MUTATION ANALYSIS"
[1] 3
  SYT17 MUTATED SYT17 WILD-TYPE 
              5              20 
  SYT17 MUTATED SYT17 WILD-TYPE 
              5              20 
[1] "ASB15 MUTATION ANALYSIS"
[1] 3
  ASB15 MUTATED ASB15 WILD-TYPE 
              8              17 
  ASB15 MUTATED ASB15 WILD-TYPE 
              8              17 
[1] "OR4A15 MUTATION ANALYSIS"
[1] 3
  OR4A15 MUTATED OR4A15 WILD-TYPE 
               6               19 
  OR4A15 MUTATED OR4A15 WILD-TYPE 
               6               19 
[1] "PROL1 MUTATION ANALYSIS"
[1] 3
  PROL1 MUTATED PROL1 WILD-TYPE 
              7              18 
  PROL1 MUTATED PROL1 WILD-TYPE 
              7              18 
[1] "DSG3 MUTATION ANALYSIS"
[1] 3
  DSG3 MUTATED DSG3 WILD-TYPE 
            13             12 
  DSG3 MUTATED DSG3 WILD-TYPE 
            13             12 
[1] "OPRK1 MUTATION ANALYSIS"
[1] 3
  OPRK1 MUTATED OPRK1 WILD-TYPE 
              9              16 
  OPRK1 MUTATED OPRK1 WILD-TYPE 
              9              16 
[1] "PCSK5 MUTATION ANALYSIS"
[1] 3
  PCSK5 MUTATED PCSK5 WILD-TYPE 
             10              15 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
             10              15 
[1] "OR52A1 MUTATION ANALYSIS"
[1] 3
  OR52A1 MUTATED OR52A1 WILD-TYPE 
               6               19 
  OR52A1 MUTATED OR52A1 WILD-TYPE 
               6               19 
[1] "ACSM2B MUTATION ANALYSIS"
[1] 3
  ACSM2B MUTATED ACSM2B WILD-TYPE 
               8               17 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
               8               17 
[1] "NOL4 MUTATION ANALYSIS"
[1] 3
  NOL4 MUTATED NOL4 WILD-TYPE 
            11             14 
  NOL4 MUTATED NOL4 WILD-TYPE 
            11             14 
[1] "PPFIA2 MUTATION ANALYSIS"
[1] 3
  PPFIA2 MUTATED PPFIA2 WILD-TYPE 
               9               16 
  PPFIA2 MUTATED PPFIA2 WILD-TYPE 
               9               16 
[1] "IL1F8 MUTATION ANALYSIS"
[1] 3
  IL1F8 MUTATED IL1F8 WILD-TYPE 
              5              20 
  IL1F8 MUTATED IL1F8 WILD-TYPE 
              5              20 
[1] "UGT2A1 MUTATION ANALYSIS"
[1] 3
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
               6               19 
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
               6               19 
[1] "SYT13 MUTATION ANALYSIS"
[1] 3
  SYT13 MUTATED SYT13 WILD-TYPE 
              3              22 
  SYT13 MUTATED SYT13 WILD-TYPE 
              3              22 
[1] "ASAH2 MUTATION ANALYSIS"
[1] 3
  ASAH2 MUTATED ASAH2 WILD-TYPE 
              6              19 
  ASAH2 MUTATED ASAH2 WILD-TYPE 
              6              19 
[1] "ZNF679 MUTATION ANALYSIS"
[1] 3
  ZNF679 MUTATED ZNF679 WILD-TYPE 
               7               18 
  ZNF679 MUTATED ZNF679 WILD-TYPE 
               7               18 
[1] "C10ORF54 MUTATION ANALYSIS"
[1] 3
  C10ORF54 MUTATED C10ORF54 WILD-TYPE 
                 4                 21 
  C10ORF54 MUTATED C10ORF54 WILD-TYPE 
                 4                 21 
[1] "C10ORF120 MUTATION ANALYSIS"
[1] 3
  C10ORF120 MUTATED C10ORF120 WILD-TYPE 
                  6                  19 
  C10ORF120 MUTATED C10ORF120 WILD-TYPE 
                  6                  19 
[1] "CHSY1 MUTATION ANALYSIS"
[1] 3
  CHSY1 MUTATED CHSY1 WILD-TYPE 
              4              21 
  CHSY1 MUTATED CHSY1 WILD-TYPE 
              4              21 
[1] "CSF2RA MUTATION ANALYSIS"
[1] 3
  CSF2RA MUTATED CSF2RA WILD-TYPE 
               6               19 
  CSF2RA MUTATED CSF2RA WILD-TYPE 
               6               19 
[1] "KCND2 MUTATION ANALYSIS"
[1] 3
  KCND2 MUTATED KCND2 WILD-TYPE 
              8              17 
  KCND2 MUTATED KCND2 WILD-TYPE 
              8              17 
[1] "SPEF2 MUTATION ANALYSIS"
[1] 3
  SPEF2 MUTATED SPEF2 WILD-TYPE 
             11              14 
  SPEF2 MUTATED SPEF2 WILD-TYPE 
             11              14 
[1] "RPGRIP1 MUTATION ANALYSIS"
[1] 3
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
                6                19 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
                6                19 
[1] "OR2L3 MUTATION ANALYSIS"
[1] 3
  OR2L3 MUTATED OR2L3 WILD-TYPE 
              3              22 
  OR2L3 MUTATED OR2L3 WILD-TYPE 
              3              22 
[1] "CCDC54 MUTATION ANALYSIS"
[1] 3
  CCDC54 MUTATED CCDC54 WILD-TYPE 
               5               20 
  CCDC54 MUTATED CCDC54 WILD-TYPE 
               5               20 
[1] "KLHL14 MUTATION ANALYSIS"
[1] 3
  KLHL14 MUTATED KLHL14 WILD-TYPE 
               5               20 
  KLHL14 MUTATED KLHL14 WILD-TYPE 
               5               20 
[1] "ZFX MUTATION ANALYSIS"
[1] 3
  ZFX MUTATED ZFX WILD-TYPE 
            7            18 
  ZFX MUTATED ZFX WILD-TYPE 
            7            18 
[1] "KLHL13 MUTATION ANALYSIS"
[1] 3
  KLHL13 MUTATED KLHL13 WILD-TYPE 
              10               15 
  KLHL13 MUTATED KLHL13 WILD-TYPE 
              10               15 
[1] "NSUN7 MUTATION ANALYSIS"
[1] 3
  NSUN7 MUTATED NSUN7 WILD-TYPE 
              3              22 
  NSUN7 MUTATED NSUN7 WILD-TYPE 
              3              22 
[1] "VEGFC MUTATION ANALYSIS"
[1] 3
  VEGFC MUTATED VEGFC WILD-TYPE 
              6              19 
  VEGFC MUTATED VEGFC WILD-TYPE 
              6              19 
[1] "TMEM202 MUTATION ANALYSIS"
[1] 3
  TMEM202 MUTATED TMEM202 WILD-TYPE 
                5                20 
  TMEM202 MUTATED TMEM202 WILD-TYPE 
                5                20 
[1] "ERC2 MUTATION ANALYSIS"
[1] 3
  ERC2 MUTATED ERC2 WILD-TYPE 
            12             13 
  ERC2 MUTATED ERC2 WILD-TYPE 
            12             13 
[1] "GRM3 MUTATION ANALYSIS"
[1] 3
  GRM3 MUTATED GRM3 WILD-TYPE 
            10             15 
  GRM3 MUTATED GRM3 WILD-TYPE 
            10             15 
[1] "CDH12 MUTATION ANALYSIS"
[1] 3
  CDH12 MUTATED CDH12 WILD-TYPE 
              8              17 
  CDH12 MUTATED CDH12 WILD-TYPE 
              8              17 
[1] "SIRPB1 MUTATION ANALYSIS"
[1] 3
  SIRPB1 MUTATED SIRPB1 WILD-TYPE 
               6               19 
  SIRPB1 MUTATED SIRPB1 WILD-TYPE 
               6               19 
[1] "data2feature, selection=ALL"
 [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 25 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
         939           NA           NA           NA           NA           NA 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO 
          NA           NA           NA          727           NA           NA 
TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE 
          NA           NA           NA           NA           NA           NA 
TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 
          NA           NA           NA           NA           NA            6 
TCGA-GN-A266 
          NA 
Variable 1:'AGE':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=12,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=12,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=7,	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"                  "LYMPH.NODE.METASTASIS"  
[5] "TUMOR.STAGECODE"         "NEOPLASM.DISEASESTAGE"  
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
T1A T2A  T3 T3A T3B  T4 T4B  TX 
  3   1   2   2   4   2   7   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 25 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=16, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=7, binary=FALSE, numeric=FALSE

Clustering(1) Variable = NRAS MUTATION ANALYSIS
D1V1, survival
                sevent
clus2            0 1
  NRAS MUTATED   1 3
  NRAS WILD-TYPE 2 7
  NRAS MUTATED NRAS WILD-TYPE 
             4              9 
  NRAS MUTATED NRAS WILD-TYPE 
             3              7 
$`NRAS MUTATED`
TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A2A2 
       11.57         1.08         2.43        23.90 

$`NRAS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29N 
       30.87        10.03         6.64         1.12         1.35         9.47 
TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
       11.11         0.20        10.09 

  NRAS MUTATED NRAS WILD-TYPE 
          1.08           0.20 
  NRAS MUTATED NRAS WILD-TYPE 
         23.90          30.87 
  NRAS MUTATED NRAS WILD-TYPE 
          7.00           9.47 
[1] "1.1 - 23.9 (7.0)" "0.2 - 30.9 (9.5)"
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
  "NRAS MUTATED"   "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GN-A266 
"NRAS WILD-TYPE" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
  "NRAS MUTATED"   "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GN-A266 
"NRAS WILD-TYPE" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
  "NRAS MUTATED"   "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GN-A266 
"NRAS WILD-TYPE" 
[1] "hr=" "1.4"
D1V2, continuous
                vv
clus             DISTANT METASTASIS
  NRAS MUTATED                    4
  NRAS WILD-TYPE                  3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  NRAS MUTATED                                                                                          0
  NRAS WILD-TYPE                                                                                        5
                vv
clus             REGIONAL LYMPH NODE
  NRAS MUTATED                     4
  NRAS WILD-TYPE                   9
D1V3, multiclass
                                                                                          clus
vv                                                                                         NRAS MUTATED
  DISTANT METASTASIS                                                                                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            0
  REGIONAL LYMPH NODE                                                                                 4
                                                                                          clus
vv                                                                                         NRAS WILD-TYPE
  DISTANT METASTASIS                                                                                    3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              5
  REGIONAL LYMPH NODE                                                                                   9
D1V4, binary
                cls
clus              0  1
  NRAS MUTATED    3  5
  NRAS WILD-TYPE  5 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      3    5
  NRAS WILD-TYPE    5   12
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            3              5
  MALE              5             12
                vv
clus             N0 N1B N2C N3
  NRAS MUTATED    3   2   1  1
  NRAS WILD-TYPE 13   1   1  1
D1V5, multiclass
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  N0             3             13
  N1B            2              1
  N2C            1              1
  N3             1              1
D1V6, continuous
                vv
clus             STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  NRAS MUTATED          1        0        1         1          2          2
  NRAS WILD-TYPE        2        1        5         2          1          2
                vv
clus             STAGE IV
  NRAS MUTATED          0
  NRAS WILD-TYPE        1
D1V7, multiclass

Clustering(2) Variable = TPTE MUTATION ANALYSIS
D2V1, survival
                sevent
clus2            0 1
  TPTE MUTATED   0 4
  TPTE WILD-TYPE 3 6
  TPTE MUTATED TPTE WILD-TYPE 
             4              9 
  TPTE MUTATED TPTE WILD-TYPE 
             4              6 
$`TPTE MUTATED`
TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N TCGA-GN-A266 
        1.35         1.08         9.47        10.09 

$`TPTE WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29V 
       30.87        10.03         6.64        11.57         1.12         2.43 
TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 
       23.90        11.11         0.20 

  TPTE MUTATED TPTE WILD-TYPE 
          1.08           0.20 
  TPTE MUTATED TPTE WILD-TYPE 
         10.09          30.87 
  TPTE MUTATED TPTE WILD-TYPE 
          5.41          10.03 
[1] "1.1 - 10.1 (5.4)"  "0.2 - 30.9 (10.0)"
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
"TPTE WILD-TYPE"   "TPTE MUTATED"   "TPTE MUTATED"   "TPTE MUTATED" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-GN-A266 
  "TPTE MUTATED" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
"TPTE WILD-TYPE"   "TPTE MUTATED"   "TPTE MUTATED"   "TPTE MUTATED" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-GN-A266 
  "TPTE MUTATED" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
"TPTE WILD-TYPE"   "TPTE MUTATED"   "TPTE MUTATED"   "TPTE MUTATED" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" "TPTE WILD-TYPE" 
    TCGA-GN-A266 
  "TPTE MUTATED" 
[1] "hr=" "3"  
D2V2, continuous
                vv
clus             DISTANT METASTASIS
  TPTE MUTATED                    4
  TPTE WILD-TYPE                  3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  TPTE MUTATED                                                                                          3
  TPTE WILD-TYPE                                                                                        2
                vv
clus             REGIONAL LYMPH NODE
  TPTE MUTATED                     7
  TPTE WILD-TYPE                   6
D2V3, multiclass
                                                                                          clus
vv                                                                                         TPTE MUTATED
  DISTANT METASTASIS                                                                                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            3
  REGIONAL LYMPH NODE                                                                                 7
                                                                                          clus
vv                                                                                         TPTE WILD-TYPE
  DISTANT METASTASIS                                                                                    3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              2
  REGIONAL LYMPH NODE                                                                                   6
D2V4, binary
                cls
clus             0 1
  TPTE MUTATED   6 8
  TPTE WILD-TYPE 2 9
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED      6    8
  TPTE WILD-TYPE    2    9
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  FEMALE            6              2
  MALE              8              9
                vv
clus             N0 N1B N2C N3
  TPTE MUTATED    9   1   1  1
  TPTE WILD-TYPE  7   2   1  1
D2V5, multiclass
     clus
vv    TPTE MUTATED TPTE WILD-TYPE
  N0             9              7
  N1B            1              2
  N2C            1              1
  N3             1              1
D2V6, continuous
                vv
clus             STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  TPTE MUTATED          1        1        5         1          1          2
  TPTE WILD-TYPE        2        0        1         2          2          2
                vv
clus             STAGE IV
  TPTE MUTATED          0
  TPTE WILD-TYPE        1
D2V7, multiclass

Clustering(3) Variable = TP53 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2            0 1
  TP53 MUTATED   1 4
  TP53 WILD-TYPE 2 6
  TP53 MUTATED TP53 WILD-TYPE 
             5              8 
  TP53 MUTATED TP53 WILD-TYPE 
             4              6 
$`TP53 MUTATED`
TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A2A2 TCGA-GN-A266 
        1.12         1.08         2.43        23.90        10.09 

$`TP53 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29N 
       30.87        10.03         6.64        11.57         1.35         9.47 
TCGA-ER-A19F TCGA-FW-A3I3 
       11.11         0.20 

  TP53 MUTATED TP53 WILD-TYPE 
          1.08           0.20 
  TP53 MUTATED TP53 WILD-TYPE 
         23.90          30.87 
  TP53 MUTATED TP53 WILD-TYPE 
          2.43           9.75 
[1] "1.1 - 23.9 (2.4)" "0.2 - 30.9 (9.8)"
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-GN-A266 
  "TP53 MUTATED" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-GN-A266 
  "TP53 MUTATED" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-GN-A266 
  "TP53 MUTATED" 
[1] "hr=" "1.4"
D3V2, continuous
                vv
clus             DISTANT METASTASIS
  TP53 MUTATED                    1
  TP53 WILD-TYPE                  6
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  TP53 MUTATED                                                                                          1
  TP53 WILD-TYPE                                                                                        4
                vv
clus             REGIONAL LYMPH NODE
  TP53 MUTATED                     5
  TP53 WILD-TYPE                   8
D3V3, multiclass
                                                                                          clus
vv                                                                                         TP53 MUTATED
  DISTANT METASTASIS                                                                                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            1
  REGIONAL LYMPH NODE                                                                                 5
                                                                                          clus
vv                                                                                         TP53 WILD-TYPE
  DISTANT METASTASIS                                                                                    6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              4
  REGIONAL LYMPH NODE                                                                                   8
D3V4, binary
                cls
clus              0  1
  TP53 MUTATED    2  5
  TP53 WILD-TYPE  6 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2    5
  TP53 WILD-TYPE    6   12
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            2              6
  MALE              5             12
                vv
clus             N0 N1B N2C N3
  TP53 MUTATED    3   2   0  1
  TP53 WILD-TYPE 13   1   2  1
D3V5, multiclass
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  N0             3             13
  N1B            2              1
  N2C            0              2
  N3             1              1
D3V6, continuous
                vv
clus             STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  TP53 MUTATED          1        0        1         1          1          2
  TP53 WILD-TYPE        2        1        5         2          2          2
                vv
clus             STAGE IV
  TP53 MUTATED          0
  TP53 WILD-TYPE        1
D3V7, multiclass

Clustering(4) Variable = GRXCR1 MUTATION ANALYSIS
D4V1, survival
                  sevent
clus2              0 1
  GRXCR1 MUTATED   0 1
  GRXCR1 WILD-TYPE 3 9
  GRXCR1 MUTATED GRXCR1 WILD-TYPE 
               1               12 
  GRXCR1 MUTATED GRXCR1 WILD-TYPE 
               1                9 
$`GRXCR1 MUTATED`
TCGA-EE-A29L 
        1.08 

$`GRXCR1 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       30.87        10.03         6.64        11.57         1.12         1.35 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        9.47         2.43        23.90        11.11         0.20        10.09 

  GRXCR1 MUTATED GRXCR1 WILD-TYPE 
            1.08             0.20 
  GRXCR1 MUTATED GRXCR1 WILD-TYPE 
            1.08            30.87 
  GRXCR1 MUTATED GRXCR1 WILD-TYPE 
            1.08             9.75 
[1] "1.1 - 1.1 (1.1)"  "0.2 - 30.9 (9.8)"
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE"   "GRXCR1 MUTATED" "GRXCR1 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-GN-A266 
"GRXCR1 WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE"   "GRXCR1 MUTATED" "GRXCR1 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-GN-A266 
"GRXCR1 WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE"   "GRXCR1 MUTATED" "GRXCR1 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-GN-A266 
"GRXCR1 WILD-TYPE" 
[1] "Remove cluster labels:" "GRXCR1 MUTATED"        
clus
  GRXCR1 MUTATED GRXCR1 WILD-TYPE 
               1               12 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29N       TCGA-EE-A29V 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3       TCGA-GN-A266 
"GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" "GRXCR1 WILD-TYPE" 
D4V2, continuous
                  vv
clus               DISTANT METASTASIS
  GRXCR1 MUTATED                    1
  GRXCR1 WILD-TYPE                  6
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  GRXCR1 MUTATED                                                                                          1
  GRXCR1 WILD-TYPE                                                                                        4
                  vv
clus               REGIONAL LYMPH NODE
  GRXCR1 MUTATED                     5
  GRXCR1 WILD-TYPE                   8
D4V3, multiclass
                                                                                          clus
vv                                                                                         GRXCR1 MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   5
                                                                                          clus
vv                                                                                         GRXCR1 WILD-TYPE
  DISTANT METASTASIS                                                                                      6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                     8
D4V4, binary
                  cls
clus                0  1
  GRXCR1 MUTATED    3  4
  GRXCR1 WILD-TYPE  5 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRXCR1 MUTATED      3    4
  GRXCR1 WILD-TYPE    5   13
        clus
vv       GRXCR1 MUTATED GRXCR1 WILD-TYPE
  FEMALE              3                5
  MALE                4               13
                  vv
clus               N0 N1B N2C N3
  GRXCR1 MUTATED    6   0   0  1
  GRXCR1 WILD-TYPE 10   3   2  1
D4V5, multiclass
     clus
vv    GRXCR1 MUTATED GRXCR1 WILD-TYPE
  N0               6               10
  N1B              0                3
  N2C              0                2
  N3               1                1
D4V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  GRXCR1 MUTATED          1        0        3         2          0          1
  GRXCR1 WILD-TYPE        2        1        3         1          3          3
                  vv
clus               STAGE IV
  GRXCR1 MUTATED          0
  GRXCR1 WILD-TYPE        1
D4V7, multiclass

Clustering(5) Variable = BRAF MUTATION ANALYSIS
D5V1, survival
                sevent
clus2            0 1
  BRAF MUTATED   0 4
  BRAF WILD-TYPE 3 6
  BRAF MUTATED BRAF WILD-TYPE 
             4              9 
  BRAF MUTATED BRAF WILD-TYPE 
             4              6 
$`BRAF MUTATED`
TCGA-DA-A1I0 TCGA-EE-A181 TCGA-EE-A29N TCGA-ER-A19F 
       10.03         1.12         9.47        11.11 

$`BRAF WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29V 
       30.87         6.64        11.57         1.35         1.08         2.43 
TCGA-EE-A2A2 TCGA-FW-A3I3 TCGA-GN-A266 
       23.90         0.20        10.09 

  BRAF MUTATED BRAF WILD-TYPE 
          1.12           0.20 
  BRAF MUTATED BRAF WILD-TYPE 
         11.11          30.87 
  BRAF MUTATED BRAF WILD-TYPE 
          9.75           6.64 
[1] "1.1 - 11.1 (9.8)" "0.2 - 30.9 (6.6)"
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"BRAF WILD-TYPE"   "BRAF MUTATED" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "BRAF MUTATED" "BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" "BRAF WILD-TYPE" 
    TCGA-GN-A266 
"BRAF WILD-TYPE" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"BRAF WILD-TYPE"   "BRAF MUTATED" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "BRAF MUTATED" "BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" "BRAF WILD-TYPE" 
    TCGA-GN-A266 
"BRAF WILD-TYPE" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"BRAF WILD-TYPE"   "BRAF MUTATED" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "BRAF MUTATED" "BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" "BRAF WILD-TYPE" 
    TCGA-GN-A266 
"BRAF WILD-TYPE" 
[1] "hr=" "1.7"
D5V2, continuous
                vv
clus             DISTANT METASTASIS
  BRAF MUTATED                    1
  BRAF WILD-TYPE                  6
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  BRAF MUTATED                                                                                          2
  BRAF WILD-TYPE                                                                                        3
                vv
clus             REGIONAL LYMPH NODE
  BRAF MUTATED                     4
  BRAF WILD-TYPE                   9
D5V3, multiclass
                                                                                          clus
vv                                                                                         BRAF MUTATED
  DISTANT METASTASIS                                                                                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            2
  REGIONAL LYMPH NODE                                                                                 4
                                                                                          clus
vv                                                                                         BRAF WILD-TYPE
  DISTANT METASTASIS                                                                                    6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              3
  REGIONAL LYMPH NODE                                                                                   9
D5V4, binary
                cls
clus              0  1
  BRAF MUTATED    3  4
  BRAF WILD-TYPE  5 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      3    4
  BRAF WILD-TYPE    5   13
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE            3              5
  MALE              4             13
                vv
clus             N0 N1B N2C N3
  BRAF MUTATED    6   0   0  1
  BRAF WILD-TYPE 10   3   2  1
D5V5, multiclass
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  N0             6             10
  N1B            0              3
  N2C            0              2
  N3             1              1
D5V6, continuous
                vv
clus             STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  BRAF MUTATED          0        0        2         2          0          1
  BRAF WILD-TYPE        3        1        4         1          3          3
                vv
clus             STAGE IV
  BRAF MUTATED          0
  BRAF WILD-TYPE        1
D5V7, multiclass

Clustering(6) Variable = TRAT1 MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2             0 1
  TRAT1 MUTATED   0 4
  TRAT1 WILD-TYPE 3 6
  TRAT1 MUTATED TRAT1 WILD-TYPE 
              4               9 
  TRAT1 MUTATED TRAT1 WILD-TYPE 
              4               6 
$`TRAT1 MUTATED`
TCGA-DA-A1IC TCGA-EE-A181 TCGA-ER-A19F TCGA-GN-A266 
        6.64         1.12        11.11        10.09 

$`TRAT1 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
       30.87        10.03        11.57         1.35         1.08         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-FW-A3I3 
        2.43        23.90         0.20 

  TRAT1 MUTATED TRAT1 WILD-TYPE 
           1.12            0.20 
  TRAT1 MUTATED TRAT1 WILD-TYPE 
          11.11           30.87 
  TRAT1 MUTATED TRAT1 WILD-TYPE 
          8.365           9.470 
[1] "1.1 - 11.1 (8.4)" "0.2 - 30.9 (9.5)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"TRAT1 WILD-TYPE" "TRAT1 WILD-TYPE"   "TRAT1 MUTATED" "TRAT1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "TRAT1 MUTATED" "TRAT1 WILD-TYPE" "TRAT1 WILD-TYPE" "TRAT1 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"TRAT1 WILD-TYPE" "TRAT1 WILD-TYPE"   "TRAT1 MUTATED" "TRAT1 WILD-TYPE" 
     TCGA-GN-A266 
  "TRAT1 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"TRAT1 WILD-TYPE" "TRAT1 WILD-TYPE"   "TRAT1 MUTATED" "TRAT1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "TRAT1 MUTATED" "TRAT1 WILD-TYPE" "TRAT1 WILD-TYPE" "TRAT1 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"TRAT1 WILD-TYPE" "TRAT1 WILD-TYPE"   "TRAT1 MUTATED" "TRAT1 WILD-TYPE" 
     TCGA-GN-A266 
  "TRAT1 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"TRAT1 WILD-TYPE" "TRAT1 WILD-TYPE"   "TRAT1 MUTATED" "TRAT1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "TRAT1 MUTATED" "TRAT1 WILD-TYPE" "TRAT1 WILD-TYPE" "TRAT1 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"TRAT1 WILD-TYPE" "TRAT1 WILD-TYPE"   "TRAT1 MUTATED" "TRAT1 WILD-TYPE" 
     TCGA-GN-A266 
  "TRAT1 MUTATED" 
[1] "hr=" "1.6"
D6V2, continuous
                 vv
clus              DISTANT METASTASIS
  TRAT1 MUTATED                    1
  TRAT1 WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  TRAT1 MUTATED                                                                                          2
  TRAT1 WILD-TYPE                                                                                        3
                 vv
clus              REGIONAL LYMPH NODE
  TRAT1 MUTATED                     4
  TRAT1 WILD-TYPE                   9
D6V3, multiclass
                                                                                          clus
vv                                                                                         TRAT1 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  4
                                                                                          clus
vv                                                                                         TRAT1 WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    9
D6V4, binary
                 cls
clus               0  1
  TRAT1 MUTATED    3  4
  TRAT1 WILD-TYPE  5 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAT1 MUTATED      3    4
  TRAT1 WILD-TYPE    5   13
        clus
vv       TRAT1 MUTATED TRAT1 WILD-TYPE
  FEMALE             3               5
  MALE               4              13
                 vv
clus              N0 N1B N2C N3
  TRAT1 MUTATED    5   0   1  0
  TRAT1 WILD-TYPE 11   3   1  2
D6V5, multiclass
     clus
vv    TRAT1 MUTATED TRAT1 WILD-TYPE
  N0              5              11
  N1B             0               3
  N2C             1               1
  N3              0               2
D6V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  TRAT1 MUTATED          1        1        1         1          1          0
  TRAT1 WILD-TYPE        2        0        5         2          2          4
                 vv
clus              STAGE IV
  TRAT1 MUTATED          0
  TRAT1 WILD-TYPE        1
D6V7, multiclass

Clustering(7) Variable = ZNF585B MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2               0 1
  ZNF585B MUTATED   0 3
  ZNF585B WILD-TYPE 3 7
  ZNF585B MUTATED ZNF585B WILD-TYPE 
                3                10 
  ZNF585B MUTATED ZNF585B WILD-TYPE 
                3                 7 
$`ZNF585B MUTATED`
TCGA-EE-A181 TCGA-EE-A29L TCGA-ER-A19F 
        1.12         1.08        11.11 

$`ZNF585B WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29N 
       30.87        10.03         6.64        11.57         1.35         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-FW-A3I3 TCGA-GN-A266 
        2.43        23.90         0.20        10.09 

  ZNF585B MUTATED ZNF585B WILD-TYPE 
             1.08              0.20 
  ZNF585B MUTATED ZNF585B WILD-TYPE 
            11.11             30.87 
  ZNF585B MUTATED ZNF585B WILD-TYPE 
             1.12              9.75 
[1] "1.1 - 11.1 (1.1)" "0.2 - 30.9 (9.8)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"ZNF585B WILD-TYPE" "ZNF585B WILD-TYPE" "ZNF585B WILD-TYPE" "ZNF585B WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "ZNF585B MUTATED" "ZNF585B WILD-TYPE"   "ZNF585B MUTATED" "ZNF585B WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"ZNF585B WILD-TYPE" "ZNF585B WILD-TYPE"   "ZNF585B MUTATED" "ZNF585B WILD-TYPE" 
       TCGA-GN-A266 
"ZNF585B WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"ZNF585B WILD-TYPE" "ZNF585B WILD-TYPE" "ZNF585B WILD-TYPE" "ZNF585B WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "ZNF585B MUTATED" "ZNF585B WILD-TYPE"   "ZNF585B MUTATED" "ZNF585B WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"ZNF585B WILD-TYPE" "ZNF585B WILD-TYPE"   "ZNF585B MUTATED" "ZNF585B WILD-TYPE" 
       TCGA-GN-A266 
"ZNF585B WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"ZNF585B WILD-TYPE" "ZNF585B WILD-TYPE" "ZNF585B WILD-TYPE" "ZNF585B WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "ZNF585B MUTATED" "ZNF585B WILD-TYPE"   "ZNF585B MUTATED" "ZNF585B WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"ZNF585B WILD-TYPE" "ZNF585B WILD-TYPE"   "ZNF585B MUTATED" "ZNF585B WILD-TYPE" 
       TCGA-GN-A266 
"ZNF585B WILD-TYPE" 
[1] "hr=" "2.5"
D7V2, continuous
                   vv
clus                DISTANT METASTASIS
  ZNF585B MUTATED                    0
  ZNF585B WILD-TYPE                  7
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ZNF585B MUTATED                                                                                          0
  ZNF585B WILD-TYPE                                                                                        5
                   vv
clus                REGIONAL LYMPH NODE
  ZNF585B MUTATED                     8
  ZNF585B WILD-TYPE                   5
D7V3, multiclass
                                                                                          clus
vv                                                                                         ZNF585B MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    8
                                                                                          clus
vv                                                                                         ZNF585B WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 5
  REGIONAL LYMPH NODE                                                                                      5
D7V4, binary
                   cls
clus                 0  1
  ZNF585B MUTATED    2  6
  ZNF585B WILD-TYPE  6 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585B MUTATED      2    6
  ZNF585B WILD-TYPE    6   11
        clus
vv       ZNF585B MUTATED ZNF585B WILD-TYPE
  FEMALE               2                 6
  MALE                 6                11
                   vv
clus                N0 N1B N2C N3
  ZNF585B MUTATED    7   0   0  1
  ZNF585B WILD-TYPE  9   3   2  1
D7V5, multiclass
     clus
vv    ZNF585B MUTATED ZNF585B WILD-TYPE
  N0                7                 9
  N1B               0                 3
  N2C               0                 2
  N3                1                 1
D7V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  ZNF585B MUTATED          1        0        3         2          0          1
  ZNF585B WILD-TYPE        2        1        3         1          3          3
                   vv
clus                STAGE IV
  ZNF585B MUTATED          0
  ZNF585B WILD-TYPE        1
D7V7, multiclass

Clustering(8) Variable = TPTE2 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2             0 1
  TPTE2 MUTATED   1 4
  TPTE2 WILD-TYPE 2 6
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              5               8 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              4               6 
$`TPTE2 MUTATED`
TCGA-D3-A2JF TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29V TCGA-ER-A19F 
       30.87        11.57         1.12         2.43        11.11 

$`TPTE2 WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A2A2 
       10.03         6.64         1.35         1.08         9.47        23.90 
TCGA-FW-A3I3 TCGA-GN-A266 
        0.20        10.09 

  TPTE2 MUTATED TPTE2 WILD-TYPE 
           1.12            0.20 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
          30.87           23.90 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
         11.110           8.055 
[1] "1.1 - 30.9 (11.1)" "0.2 - 23.9 (8.1)" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "TPTE2 MUTATED" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE"   "TPTE2 MUTATED" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "TPTE2 MUTATED" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "TPTE2 MUTATED" "TPTE2 WILD-TYPE"   "TPTE2 MUTATED" "TPTE2 WILD-TYPE" 
     TCGA-GN-A266 
"TPTE2 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "TPTE2 MUTATED" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE"   "TPTE2 MUTATED" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "TPTE2 MUTATED" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "TPTE2 MUTATED" "TPTE2 WILD-TYPE"   "TPTE2 MUTATED" "TPTE2 WILD-TYPE" 
     TCGA-GN-A266 
"TPTE2 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "TPTE2 MUTATED" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE"   "TPTE2 MUTATED" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "TPTE2 MUTATED" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "TPTE2 MUTATED" "TPTE2 WILD-TYPE"   "TPTE2 MUTATED" "TPTE2 WILD-TYPE" 
     TCGA-GN-A266 
"TPTE2 WILD-TYPE" 
[1] "hr=" "1.6"
D8V2, continuous
                 vv
clus              DISTANT METASTASIS
  TPTE2 MUTATED                    4
  TPTE2 WILD-TYPE                  3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  TPTE2 MUTATED                                                                                          2
  TPTE2 WILD-TYPE                                                                                        3
                 vv
clus              REGIONAL LYMPH NODE
  TPTE2 MUTATED                     5
  TPTE2 WILD-TYPE                   8
D8V3, multiclass
                                                                                          clus
vv                                                                                         TPTE2 MUTATED
  DISTANT METASTASIS                                                                                   4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  5
                                                                                          clus
vv                                                                                         TPTE2 WILD-TYPE
  DISTANT METASTASIS                                                                                     3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    8
D8V4, binary
                 cls
clus               0  1
  TPTE2 MUTATED    4  7
  TPTE2 WILD-TYPE  4 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      4    7
  TPTE2 WILD-TYPE    4   10
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  FEMALE             4               4
  MALE               7              10
                 vv
clus              N0 N1B N2C N3
  TPTE2 MUTATED    9   1   0  0
  TPTE2 WILD-TYPE  7   2   2  2
D8V5, multiclass
     clus
vv    TPTE2 MUTATED TPTE2 WILD-TYPE
  N0              9               7
  N1B             1               2
  N2C             0               2
  N3              0               2
D8V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  TPTE2 MUTATED          2        1        4         1          0          1
  TPTE2 WILD-TYPE        1        0        2         2          3          3
                 vv
clus              STAGE IV
  TPTE2 MUTATED          0
  TPTE2 WILD-TYPE        1
D8V7, multiclass

Clustering(9) Variable = OR51S1 MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2              0 1
  OR51S1 MUTATED   0 2
  OR51S1 WILD-TYPE 3 8
  OR51S1 MUTATED OR51S1 WILD-TYPE 
               2               11 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
               2                8 
$`OR51S1 MUTATED`
TCGA-EE-A29N TCGA-GN-A266 
        9.47        10.09 

$`OR51S1 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       30.87        10.03         6.64        11.57         1.12         1.35 
TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 
        1.08         2.43        23.90        11.11         0.20 

  OR51S1 MUTATED OR51S1 WILD-TYPE 
            9.47             0.20 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
           10.09            30.87 
  OR51S1 MUTATED OR51S1 WILD-TYPE 
            9.78             6.64 
[1] "9.5 - 10.1 (9.8)" "0.2 - 30.9 (6.6)"
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE"   "OR51S1 MUTATED" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" 
      TCGA-GN-A266 
  "OR51S1 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE"   "OR51S1 MUTATED" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" 
      TCGA-GN-A266 
  "OR51S1 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE"   "OR51S1 MUTATED" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" 
      TCGA-GN-A266 
  "OR51S1 MUTATED" 
[1] "Remove cluster labels:" "OR51S1 MUTATED"        
clus
  OR51S1 MUTATED OR51S1 WILD-TYPE 
               2               11 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29V 
"OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" "OR51S1 WILD-TYPE" 
D9V2, continuous
                  vv
clus               DISTANT METASTASIS
  OR51S1 MUTATED                    1
  OR51S1 WILD-TYPE                  6
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  OR51S1 MUTATED                                                                                          2
  OR51S1 WILD-TYPE                                                                                        3
                  vv
clus               REGIONAL LYMPH NODE
  OR51S1 MUTATED                     5
  OR51S1 WILD-TYPE                   8
D9V3, multiclass
                                                                                          clus
vv                                                                                         OR51S1 MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              2
  REGIONAL LYMPH NODE                                                                                   5
                                                                                          clus
vv                                                                                         OR51S1 WILD-TYPE
  DISTANT METASTASIS                                                                                      6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     8
D9V4, binary
                  cls
clus                0  1
  OR51S1 MUTATED    2  6
  OR51S1 WILD-TYPE  6 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51S1 MUTATED      2    6
  OR51S1 WILD-TYPE    6   11
        clus
vv       OR51S1 MUTATED OR51S1 WILD-TYPE
  FEMALE              2                6
  MALE                6               11
                  vv
clus               N0 N1B N2C N3
  OR51S1 MUTATED    6   0   0  0
  OR51S1 WILD-TYPE 10   3   2  2
D9V5, multiclass
     clus
vv    OR51S1 MUTATED OR51S1 WILD-TYPE
  N0               6               10
  N1B              0                3
  N2C              0                2
  N3               0                2
D9V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  OR51S1 MUTATED          0        1        3         1          0          0
  OR51S1 WILD-TYPE        3        0        3         2          3          4
                  vv
clus               STAGE IV
  OR51S1 MUTATED          0
  OR51S1 WILD-TYPE        1
D9V7, multiclass

Clustering(10) Variable = RAC1 MUTATION ANALYSIS
D10V1, survival
                sevent
clus2            0 1
  RAC1 MUTATED   0 2
  RAC1 WILD-TYPE 3 8
  RAC1 MUTATED RAC1 WILD-TYPE 
             2             11 
  RAC1 MUTATED RAC1 WILD-TYPE 
             2              8 
$`RAC1 MUTATED`
TCGA-EE-A181 TCGA-GN-A266 
        1.12        10.09 

$`RAC1 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L 
       30.87        10.03         6.64        11.57         1.35         1.08 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 
        9.47         2.43        23.90        11.11         0.20 

  RAC1 MUTATED RAC1 WILD-TYPE 
          1.12           0.20 
  RAC1 MUTATED RAC1 WILD-TYPE 
         10.09          30.87 
  RAC1 MUTATED RAC1 WILD-TYPE 
         5.605          9.470 
[1] "1.1 - 10.1 (5.6)" "0.2 - 30.9 (9.5)"
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "RAC1 MUTATED" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-GN-A266 
  "RAC1 MUTATED" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "RAC1 MUTATED" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-GN-A266 
  "RAC1 MUTATED" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "RAC1 MUTATED" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-GN-A266 
  "RAC1 MUTATED" 
[1] "Remove cluster labels:" "RAC1 MUTATED"          
clus
  RAC1 MUTATED RAC1 WILD-TYPE 
             2             11 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N     TCGA-EE-A29V 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
D10V2, continuous
                vv
clus             DISTANT METASTASIS
  RAC1 MUTATED                    1
  RAC1 WILD-TYPE                  6
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  RAC1 MUTATED                                                                                          1
  RAC1 WILD-TYPE                                                                                        4
                vv
clus             REGIONAL LYMPH NODE
  RAC1 MUTATED                     2
  RAC1 WILD-TYPE                  11
D10V3, multiclass
                                                                                          clus
vv                                                                                         RAC1 MUTATED
  DISTANT METASTASIS                                                                                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            1
  REGIONAL LYMPH NODE                                                                                 2
                                                                                          clus
vv                                                                                         RAC1 WILD-TYPE
  DISTANT METASTASIS                                                                                    6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              4
  REGIONAL LYMPH NODE                                                                                  11
D10V4, binary
                cls
clus              0  1
  RAC1 MUTATED    2  2
  RAC1 WILD-TYPE  6 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      2    2
  RAC1 WILD-TYPE    6   15
        clus
vv       RAC1 MUTATED RAC1 WILD-TYPE
  FEMALE            2              6
  MALE              2             15
                vv
clus             N0 N1B N2C N3
  RAC1 MUTATED    2   0   1  0
  RAC1 WILD-TYPE 14   3   1  2
D10V5, multiclass
     clus
vv    RAC1 MUTATED RAC1 WILD-TYPE
  N0             2             14
  N1B            0              3
  N2C            1              1
  N3             0              2
D10V6, continuous
                vv
clus             STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  RAC1 MUTATED          0        0        2         0          1          0
  RAC1 WILD-TYPE        3        1        4         3          2          4
                vv
clus             STAGE IV
  RAC1 MUTATED          0
  RAC1 WILD-TYPE        1
D10V7, multiclass

Clustering(11) Variable = CDKN2A MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2              0 1
  CDKN2A MUTATED   1 2
  CDKN2A WILD-TYPE 2 8
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               3               10 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               2                8 
$`CDKN2A MUTATED`
TCGA-D3-A2JF TCGA-EE-A181 TCGA-EE-A29V 
       30.87         1.12         2.43 

$`CDKN2A WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
       10.03         6.64        11.57         1.35         1.08         9.47 
TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
       23.90        11.11         0.20        10.09 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            1.12             0.20 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           30.87            23.90 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
            2.43             9.75 
[1] "1.1 - 30.9 (2.4)" "0.2 - 23.9 (9.8)"
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
  "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
  "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
  "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-GN-A266 
"CDKN2A WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
  "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
  "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
  "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-GN-A266 
"CDKN2A WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
  "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
  "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
  "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-GN-A266 
"CDKN2A WILD-TYPE" 
[1] "hr=" "1.1"
D11V2, continuous
                  vv
clus               DISTANT METASTASIS
  CDKN2A MUTATED                    2
  CDKN2A WILD-TYPE                  5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CDKN2A MUTATED                                                                                          0
  CDKN2A WILD-TYPE                                                                                        5
                  vv
clus               REGIONAL LYMPH NODE
  CDKN2A MUTATED                     3
  CDKN2A WILD-TYPE                  10
D11V3, multiclass
                                                                                          clus
vv                                                                                         CDKN2A MUTATED
  DISTANT METASTASIS                                                                                    2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              0
  REGIONAL LYMPH NODE                                                                                   3
                                                                                          clus
vv                                                                                         CDKN2A WILD-TYPE
  DISTANT METASTASIS                                                                                      5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    10
D11V4, binary
                  cls
clus                0  1
  CDKN2A MUTATED    2  3
  CDKN2A WILD-TYPE  6 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      2    3
  CDKN2A WILD-TYPE    6   14
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              2                6
  MALE                3               14
                  vv
clus               N0 N1B N2C N3
  CDKN2A MUTATED    4   1   0  0
  CDKN2A WILD-TYPE 12   2   2  2
D11V5, multiclass
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  N0               4               12
  N1B              1                2
  N2C              0                2
  N3               0                2
D11V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  CDKN2A MUTATED          2        0        1         1          0          1
  CDKN2A WILD-TYPE        1        1        5         2          3          3
                  vv
clus               STAGE IV
  CDKN2A MUTATED          0
  CDKN2A WILD-TYPE        1
D11V7, multiclass

Clustering(12) Variable = C7 MUTATION ANALYSIS
D12V1, survival
              sevent
clus2          0 1
  C7 MUTATED   0 4
  C7 WILD-TYPE 3 6
  C7 MUTATED C7 WILD-TYPE 
           4            9 
  C7 MUTATED C7 WILD-TYPE 
           4            6 
$`C7 MUTATED`
TCGA-EE-A181 TCGA-EE-A182 TCGA-ER-A19F TCGA-GN-A266 
        1.12         1.35        11.11        10.09 

$`C7 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29N 
       30.87        10.03         6.64        11.57         1.08         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-FW-A3I3 
        2.43        23.90         0.20 

  C7 MUTATED C7 WILD-TYPE 
        1.12         0.20 
  C7 MUTATED C7 WILD-TYPE 
       11.11        30.87 
  C7 MUTATED C7 WILD-TYPE 
        5.72         9.47 
[1] "1.1 - 11.1 (5.7)" "0.2 - 30.9 (9.5)"
  TCGA-D3-A2JF   TCGA-DA-A1I0   TCGA-DA-A1IC   TCGA-EE-A17X   TCGA-EE-A181 
"C7 WILD-TYPE" "C7 WILD-TYPE" "C7 WILD-TYPE" "C7 WILD-TYPE"   "C7 MUTATED" 
  TCGA-EE-A182   TCGA-EE-A29L   TCGA-EE-A29N   TCGA-EE-A29V   TCGA-EE-A2A2 
  "C7 MUTATED" "C7 WILD-TYPE" "C7 WILD-TYPE" "C7 WILD-TYPE" "C7 WILD-TYPE" 
  TCGA-ER-A19F   TCGA-FW-A3I3   TCGA-GN-A266 
  "C7 MUTATED" "C7 WILD-TYPE"   "C7 MUTATED" 
  TCGA-D3-A2JF   TCGA-DA-A1I0   TCGA-DA-A1IC   TCGA-EE-A17X   TCGA-EE-A181 
"C7 WILD-TYPE" "C7 WILD-TYPE" "C7 WILD-TYPE" "C7 WILD-TYPE"   "C7 MUTATED" 
  TCGA-EE-A182   TCGA-EE-A29L   TCGA-EE-A29N   TCGA-EE-A29V   TCGA-EE-A2A2 
  "C7 MUTATED" "C7 WILD-TYPE" "C7 WILD-TYPE" "C7 WILD-TYPE" "C7 WILD-TYPE" 
  TCGA-ER-A19F   TCGA-FW-A3I3   TCGA-GN-A266 
  "C7 MUTATED" "C7 WILD-TYPE"   "C7 MUTATED" 
  TCGA-D3-A2JF   TCGA-DA-A1I0   TCGA-DA-A1IC   TCGA-EE-A17X   TCGA-EE-A181 
"C7 WILD-TYPE" "C7 WILD-TYPE" "C7 WILD-TYPE" "C7 WILD-TYPE"   "C7 MUTATED" 
  TCGA-EE-A182   TCGA-EE-A29L   TCGA-EE-A29N   TCGA-EE-A29V   TCGA-EE-A2A2 
  "C7 MUTATED" "C7 WILD-TYPE" "C7 WILD-TYPE" "C7 WILD-TYPE" "C7 WILD-TYPE" 
  TCGA-ER-A19F   TCGA-FW-A3I3   TCGA-GN-A266 
  "C7 MUTATED" "C7 WILD-TYPE"   "C7 MUTATED" 
[1] "hr=" "1.8"
D12V2, continuous
              vv
clus           DISTANT METASTASIS
  C7 MUTATED                    3
  C7 WILD-TYPE                  4
              vv
clus           REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  C7 MUTATED                                                                                          3
  C7 WILD-TYPE                                                                                        2
              vv
clus           REGIONAL LYMPH NODE
  C7 MUTATED                     5
  C7 WILD-TYPE                   8
D12V3, multiclass
                                                                                          clus
vv                                                                                         C7 MUTATED
  DISTANT METASTASIS                                                                                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)          3
  REGIONAL LYMPH NODE                                                                               5
                                                                                          clus
vv                                                                                         C7 WILD-TYPE
  DISTANT METASTASIS                                                                                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            2
  REGIONAL LYMPH NODE                                                                                 8
D12V4, binary
              cls
clus            0  1
  C7 MUTATED    6  5
  C7 WILD-TYPE  2 12
[1] "tbl2"
              cls
clus           [,1] [,2]
  C7 MUTATED      6    5
  C7 WILD-TYPE    2   12
        clus
vv       C7 MUTATED C7 WILD-TYPE
  FEMALE          6            2
  MALE            5           12
              vv
clus           N0 N1B N2C N3
  C7 MUTATED    7   1   1  0
  C7 WILD-TYPE  9   2   1  2
D12V5, multiclass
     clus
vv    C7 MUTATED C7 WILD-TYPE
  N0           7            9
  N1B          1            2
  N2C          1            1
  N3           0            2
D12V6, continuous
              vv
clus           STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  C7 MUTATED          1        0        4         1          1          1
  C7 WILD-TYPE        2        1        2         2          2          3
              vv
clus           STAGE IV
  C7 MUTATED          0
  C7 WILD-TYPE        1
D12V7, multiclass

Clustering(13) Variable = C15ORF23 MUTATION ANALYSIS
D13V1, survival
                    sevent
clus2                0 1
  C15ORF23 MUTATED   1 3
  C15ORF23 WILD-TYPE 2 7
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                 4                  9 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                 3                  7 
$`C15ORF23 MUTATED`
TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A2A2 TCGA-GN-A266 
        6.64         1.12        23.90        10.09 

$`C15ORF23 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
       30.87        10.03        11.57         1.35         1.08         9.47 
TCGA-EE-A29V TCGA-ER-A19F TCGA-FW-A3I3 
        2.43        11.11         0.20 

  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
              1.12               0.20 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
             23.90              30.87 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
             8.365              9.470 
[1] "1.1 - 23.9 (8.4)" "0.2 - 30.9 (9.5)"
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE"   "C15ORF23 MUTATED" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"C15ORF23 WILD-TYPE"   "C15ORF23 MUTATED" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-ER-A19F         TCGA-FW-A3I3 
  "C15ORF23 MUTATED" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-GN-A266 
  "C15ORF23 MUTATED" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE"   "C15ORF23 MUTATED" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"C15ORF23 WILD-TYPE"   "C15ORF23 MUTATED" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-ER-A19F         TCGA-FW-A3I3 
  "C15ORF23 MUTATED" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-GN-A266 
  "C15ORF23 MUTATED" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE"   "C15ORF23 MUTATED" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"C15ORF23 WILD-TYPE"   "C15ORF23 MUTATED" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-ER-A19F         TCGA-FW-A3I3 
  "C15ORF23 MUTATED" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-GN-A266 
  "C15ORF23 MUTATED" 
[1] "hr=" "1.2"
D13V2, continuous
                    vv
clus                 DISTANT METASTASIS
  C15ORF23 MUTATED                    0
  C15ORF23 WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  C15ORF23 MUTATED                                                                                          2
  C15ORF23 WILD-TYPE                                                                                        3
                    vv
clus                 REGIONAL LYMPH NODE
  C15ORF23 MUTATED                     3
  C15ORF23 WILD-TYPE                  10
D13V3, multiclass
                                                                                          clus
vv                                                                                         C15ORF23 MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         C15ORF23 WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  3
  REGIONAL LYMPH NODE                                                                                      10
D13V4, binary
                    cls
clus                  0  1
  C15ORF23 MUTATED    1  4
  C15ORF23 WILD-TYPE  7 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF23 MUTATED      1    4
  C15ORF23 WILD-TYPE    7   13
        clus
vv       C15ORF23 MUTATED C15ORF23 WILD-TYPE
  FEMALE                1                  7
  MALE                  4                 13
                    vv
clus                 N0 N1B N2C N3
  C15ORF23 MUTATED    2   1   1  0
  C15ORF23 WILD-TYPE 14   2   1  2
D13V5, multiclass
     clus
vv    C15ORF23 MUTATED C15ORF23 WILD-TYPE
  N0                 2                 14
  N1B                1                  2
  N2C                1                  1
  N3                 0                  2
D13V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  C15ORF23 MUTATED          0        0        1         1          2          0
  C15ORF23 WILD-TYPE        3        1        5         2          1          4
                    vv
clus                 STAGE IV
  C15ORF23 MUTATED          0
  C15ORF23 WILD-TYPE        1
D13V7, multiclass

Clustering(14) Variable = GLRB MUTATION ANALYSIS
D14V1, survival
                sevent
clus2            0 1
  GLRB MUTATED   1 2
  GLRB WILD-TYPE 2 8
  GLRB MUTATED GLRB WILD-TYPE 
             3             10 
  GLRB MUTATED GLRB WILD-TYPE 
             2              8 
$`GLRB MUTATED`
TCGA-D3-A2JF TCGA-EE-A182 TCGA-EE-A29L 
       30.87         1.35         1.08 

$`GLRB WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A29V 
       10.03         6.64        11.57         1.12         9.47         2.43 
TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
       23.90        11.11         0.20        10.09 

  GLRB MUTATED GLRB WILD-TYPE 
          1.08           0.20 
  GLRB MUTATED GLRB WILD-TYPE 
         30.87          23.90 
  GLRB MUTATED GLRB WILD-TYPE 
          1.35           9.75 
[1] "1.1 - 30.9 (1.4)" "0.2 - 23.9 (9.8)"
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
  "GLRB MUTATED" "GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
"GLRB WILD-TYPE"   "GLRB MUTATED"   "GLRB MUTATED" "GLRB WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-GN-A266 
"GLRB WILD-TYPE" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
  "GLRB MUTATED" "GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
"GLRB WILD-TYPE"   "GLRB MUTATED"   "GLRB MUTATED" "GLRB WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-GN-A266 
"GLRB WILD-TYPE" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
  "GLRB MUTATED" "GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
"GLRB WILD-TYPE"   "GLRB MUTATED"   "GLRB MUTATED" "GLRB WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-GN-A266 
"GLRB WILD-TYPE" 
[1] "hr=" "1"  
D14V2, continuous
                vv
clus             DISTANT METASTASIS
  GLRB MUTATED                    3
  GLRB WILD-TYPE                  4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  GLRB MUTATED                                                                                          0
  GLRB WILD-TYPE                                                                                        5
                vv
clus             REGIONAL LYMPH NODE
  GLRB MUTATED                     3
  GLRB WILD-TYPE                  10
D14V3, multiclass
                                                                                          clus
vv                                                                                         GLRB MUTATED
  DISTANT METASTASIS                                                                                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            0
  REGIONAL LYMPH NODE                                                                                 3
                                                                                          clus
vv                                                                                         GLRB WILD-TYPE
  DISTANT METASTASIS                                                                                    4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              5
  REGIONAL LYMPH NODE                                                                                  10
D14V4, binary
                cls
clus              0  1
  GLRB MUTATED    3  3
  GLRB WILD-TYPE  5 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLRB MUTATED      3    3
  GLRB WILD-TYPE    5   14
        clus
vv       GLRB MUTATED GLRB WILD-TYPE
  FEMALE            3              5
  MALE              3             14
                vv
clus             N0 N1B N2C N3
  GLRB MUTATED    4   1   0  1
  GLRB WILD-TYPE 12   2   2  1
D14V5, multiclass
     clus
vv    GLRB MUTATED GLRB WILD-TYPE
  N0             4             12
  N1B            1              2
  N2C            0              2
  N3             1              1
D14V6, continuous
                vv
clus             STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  GLRB MUTATED          2        0        1         1          0          2
  GLRB WILD-TYPE        1        1        5         2          3          2
                vv
clus             STAGE IV
  GLRB MUTATED          0
  GLRB WILD-TYPE        1
D14V7, multiclass

Clustering(15) Variable = FAM58A MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2              0 1
  FAM58A MUTATED   0 2
  FAM58A WILD-TYPE 3 8
  FAM58A MUTATED FAM58A WILD-TYPE 
               2               11 
  FAM58A MUTATED FAM58A WILD-TYPE 
               2                8 
$`FAM58A MUTATED`
TCGA-DA-A1IC TCGA-EE-A29N 
        6.64         9.47 

$`FAM58A WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L 
       30.87        10.03        11.57         1.12         1.35         1.08 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        2.43        23.90        11.11         0.20        10.09 

  FAM58A MUTATED FAM58A WILD-TYPE 
            6.64             0.20 
  FAM58A MUTATED FAM58A WILD-TYPE 
            9.47            30.87 
  FAM58A MUTATED FAM58A WILD-TYPE 
           8.055           10.030 
[1] "6.6 - 9.5 (8.1)"   "0.2 - 30.9 (10.0)"
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE"   "FAM58A MUTATED" "FAM58A WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE"   "FAM58A MUTATED" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" 
      TCGA-GN-A266 
"FAM58A WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE"   "FAM58A MUTATED" "FAM58A WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE"   "FAM58A MUTATED" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" 
      TCGA-GN-A266 
"FAM58A WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE"   "FAM58A MUTATED" "FAM58A WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE"   "FAM58A MUTATED" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" 
      TCGA-GN-A266 
"FAM58A WILD-TYPE" 
[1] "Remove cluster labels:" "FAM58A MUTATED"        
clus
  FAM58A MUTATED FAM58A WILD-TYPE 
               2               11 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-EE-A17X       TCGA-EE-A181 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" 
      TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29V       TCGA-EE-A2A2 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" 
      TCGA-ER-A19F       TCGA-FW-A3I3       TCGA-GN-A266 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" 
D15V2, continuous
                  vv
clus               DISTANT METASTASIS
  FAM58A MUTATED                    0
  FAM58A WILD-TYPE                  7
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  FAM58A MUTATED                                                                                          1
  FAM58A WILD-TYPE                                                                                        4
                  vv
clus               REGIONAL LYMPH NODE
  FAM58A MUTATED                     2
  FAM58A WILD-TYPE                  11
D15V3, multiclass
                                                                                          clus
vv                                                                                         FAM58A MUTATED
  DISTANT METASTASIS                                                                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   2
                                                                                          clus
vv                                                                                         FAM58A WILD-TYPE
  DISTANT METASTASIS                                                                                      7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                    11
D15V4, binary
                  cls
clus                0  1
  FAM58A MUTATED    0  3
  FAM58A WILD-TYPE  8 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM58A MUTATED      0    3
  FAM58A WILD-TYPE    8   14
        clus
vv       FAM58A MUTATED FAM58A WILD-TYPE
  FEMALE              0                8
  MALE                3               14
                  vv
clus               N0 N1B N2C N3
  FAM58A MUTATED    2   0   1  0
  FAM58A WILD-TYPE 14   3   1  2
D15V5, multiclass
     clus
vv    FAM58A MUTATED FAM58A WILD-TYPE
  N0               2               14
  N1B              0                3
  N2C              1                1
  N3               0                2
D15V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  FAM58A MUTATED          0        1        0         0          1          0
  FAM58A WILD-TYPE        3        0        6         3          2          4
                  vv
clus               STAGE IV
  FAM58A MUTATED          0
  FAM58A WILD-TYPE        1
D15V7, multiclass
[1] "Remove cluster labels:" "FAM58A MUTATED"        
clus
  FAM58A MUTATED FAM58A WILD-TYPE 
               2               19 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-EE-A17X       TCGA-EE-A181 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" 
      TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29V       TCGA-EE-A2A2 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" 
      TCGA-EE-A2GC       TCGA-EE-A2GO       TCGA-EE-A2GR       TCGA-EE-A2MI 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" 
      TCGA-EE-A2MJ       TCGA-EE-A2MS       TCGA-EE-A3AE       TCGA-FS-A1ZA 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" 
      TCGA-FS-A1ZP       TCGA-FS-A1ZZ       TCGA-FW-A3I3 
"FAM58A WILD-TYPE" "FAM58A WILD-TYPE" "FAM58A WILD-TYPE" 

Clustering(16) Variable = EPHA6 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2             0 1
  EPHA6 MUTATED   1 3
  EPHA6 WILD-TYPE 2 7
  EPHA6 MUTATED EPHA6 WILD-TYPE 
              4               9 
  EPHA6 MUTATED EPHA6 WILD-TYPE 
              3               7 
$`EPHA6 MUTATED`
TCGA-D3-A2JF TCGA-EE-A181 TCGA-EE-A29N TCGA-GN-A266 
       30.87         1.12         9.47        10.09 

$`EPHA6 WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29V 
       10.03         6.64        11.57         1.35         1.08         2.43 
TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 
       23.90        11.11         0.20 

  EPHA6 MUTATED EPHA6 WILD-TYPE 
           1.12            0.20 
  EPHA6 MUTATED EPHA6 WILD-TYPE 
          30.87           23.90 
  EPHA6 MUTATED EPHA6 WILD-TYPE 
           9.78            6.64 
[1] "1.1 - 30.9 (9.8)" "0.2 - 23.9 (6.6)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "EPHA6 MUTATED" "EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "EPHA6 MUTATED" "EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE"   "EPHA6 MUTATED" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE" 
     TCGA-GN-A266 
  "EPHA6 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "EPHA6 MUTATED" "EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "EPHA6 MUTATED" "EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE"   "EPHA6 MUTATED" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE" 
     TCGA-GN-A266 
  "EPHA6 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "EPHA6 MUTATED" "EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "EPHA6 MUTATED" "EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE"   "EPHA6 MUTATED" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE" "EPHA6 WILD-TYPE" 
     TCGA-GN-A266 
  "EPHA6 MUTATED" 
[1] "hr=" "1.2"
D16V2, continuous
                 vv
clus              DISTANT METASTASIS
  EPHA6 MUTATED                    4
  EPHA6 WILD-TYPE                  3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  EPHA6 MUTATED                                                                                          1
  EPHA6 WILD-TYPE                                                                                        4
                 vv
clus              REGIONAL LYMPH NODE
  EPHA6 MUTATED                     6
  EPHA6 WILD-TYPE                   7
D16V3, multiclass
                                                                                          clus
vv                                                                                         EPHA6 MUTATED
  DISTANT METASTASIS                                                                                   4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  6
                                                                                          clus
vv                                                                                         EPHA6 WILD-TYPE
  DISTANT METASTASIS                                                                                     3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                    7
D16V4, binary
                 cls
clus               0  1
  EPHA6 MUTATED    4  7
  EPHA6 WILD-TYPE  4 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA6 MUTATED      4    7
  EPHA6 WILD-TYPE    4   10
        clus
vv       EPHA6 MUTATED EPHA6 WILD-TYPE
  FEMALE             4               4
  MALE               7              10
                 vv
clus              N0 N1B N2C N3
  EPHA6 MUTATED    8   0   1  0
  EPHA6 WILD-TYPE  8   3   1  2
D16V5, multiclass
     clus
vv    EPHA6 MUTATED EPHA6 WILD-TYPE
  N0              8               8
  N1B             0               3
  N2C             1               1
  N3              0               2
D16V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  EPHA6 MUTATED          1        1        3         2          1          0
  EPHA6 WILD-TYPE        2        0        3         1          2          4
                 vv
clus              STAGE IV
  EPHA6 MUTATED          0
  EPHA6 WILD-TYPE        1
D16V7, multiclass

Clustering(17) Variable = NAP1L2 MUTATION ANALYSIS
D17V1, survival
                  sevent
clus2              0 1
  NAP1L2 MUTATED   0 1
  NAP1L2 WILD-TYPE 3 9
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               1               12 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               1                9 
$`NAP1L2 MUTATED`
TCGA-EE-A182 
        1.35 

$`NAP1L2 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29L 
       30.87        10.03         6.64        11.57         1.12         1.08 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        9.47         2.43        23.90        11.11         0.20        10.09 

  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
            1.35             0.20 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
            1.35            30.87 
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
            1.35             9.75 
[1] "1.4 - 1.4 (1.4)"  "0.2 - 30.9 (9.8)"
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"NAP1L2 WILD-TYPE"   "NAP1L2 MUTATED" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-GN-A266 
"NAP1L2 WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"NAP1L2 WILD-TYPE"   "NAP1L2 MUTATED" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-GN-A266 
"NAP1L2 WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"NAP1L2 WILD-TYPE"   "NAP1L2 MUTATED" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-GN-A266 
"NAP1L2 WILD-TYPE" 
[1] "Remove cluster labels:" "NAP1L2 MUTATED"        
clus
  NAP1L2 MUTATED NAP1L2 WILD-TYPE 
               1               12 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A29L       TCGA-EE-A29N       TCGA-EE-A29V 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3       TCGA-GN-A266 
"NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" "NAP1L2 WILD-TYPE" 
D17V2, continuous
                  vv
clus               DISTANT METASTASIS
  NAP1L2 MUTATED                    3
  NAP1L2 WILD-TYPE                  4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  NAP1L2 MUTATED                                                                                          2
  NAP1L2 WILD-TYPE                                                                                        3
                  vv
clus               REGIONAL LYMPH NODE
  NAP1L2 MUTATED                     2
  NAP1L2 WILD-TYPE                  11
D17V3, multiclass
                                                                                          clus
vv                                                                                         NAP1L2 MUTATED
  DISTANT METASTASIS                                                                                    3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              2
  REGIONAL LYMPH NODE                                                                                   2
                                                                                          clus
vv                                                                                         NAP1L2 WILD-TYPE
  DISTANT METASTASIS                                                                                      4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                    11
D17V4, binary
                  cls
clus                0  1
  NAP1L2 MUTATED    4  3
  NAP1L2 WILD-TYPE  4 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L2 MUTATED      4    3
  NAP1L2 WILD-TYPE    4   14
        clus
vv       NAP1L2 MUTATED NAP1L2 WILD-TYPE
  FEMALE              4                4
  MALE                3               14
                  vv
clus               N0 N1B N2C N3
  NAP1L2 MUTATED    5   1   0  0
  NAP1L2 WILD-TYPE 11   2   2  2
D17V5, multiclass
     clus
vv    NAP1L2 MUTATED NAP1L2 WILD-TYPE
  N0               5               11
  N1B              1                2
  N2C              0                2
  N3               0                2
D17V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  NAP1L2 MUTATED          0        1        3         1          0          1
  NAP1L2 WILD-TYPE        3        0        3         2          3          3
                  vv
clus               STAGE IV
  NAP1L2 MUTATED          0
  NAP1L2 WILD-TYPE        1
D17V7, multiclass

Clustering(18) Variable = OR4K5 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2             0 1
  OR4K5 MUTATED   2 3
  OR4K5 WILD-TYPE 1 7
  OR4K5 MUTATED OR4K5 WILD-TYPE 
              5               8 
  OR4K5 MUTATED OR4K5 WILD-TYPE 
              3               7 
$`OR4K5 MUTATED`
TCGA-D3-A2JF TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A2A2 
       30.87         1.35         1.08         2.43        23.90 

$`OR4K5 WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29N TCGA-ER-A19F 
       10.03         6.64        11.57         1.12         9.47        11.11 
TCGA-FW-A3I3 TCGA-GN-A266 
        0.20        10.09 

  OR4K5 MUTATED OR4K5 WILD-TYPE 
           1.08            0.20 
  OR4K5 MUTATED OR4K5 WILD-TYPE 
          30.87           11.57 
  OR4K5 MUTATED OR4K5 WILD-TYPE 
           2.43            9.75 
[1] "1.1 - 30.9 (2.4)" "0.2 - 11.6 (9.8)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "OR4K5 MUTATED" "OR4K5 WILD-TYPE" "OR4K5 WILD-TYPE" "OR4K5 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"OR4K5 WILD-TYPE"   "OR4K5 MUTATED"   "OR4K5 MUTATED" "OR4K5 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "OR4K5 MUTATED"   "OR4K5 MUTATED" "OR4K5 WILD-TYPE" "OR4K5 WILD-TYPE" 
     TCGA-GN-A266 
"OR4K5 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "OR4K5 MUTATED" "OR4K5 WILD-TYPE" "OR4K5 WILD-TYPE" "OR4K5 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"OR4K5 WILD-TYPE"   "OR4K5 MUTATED"   "OR4K5 MUTATED" "OR4K5 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "OR4K5 MUTATED"   "OR4K5 MUTATED" "OR4K5 WILD-TYPE" "OR4K5 WILD-TYPE" 
     TCGA-GN-A266 
"OR4K5 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "OR4K5 MUTATED" "OR4K5 WILD-TYPE" "OR4K5 WILD-TYPE" "OR4K5 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"OR4K5 WILD-TYPE"   "OR4K5 MUTATED"   "OR4K5 MUTATED" "OR4K5 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "OR4K5 MUTATED"   "OR4K5 MUTATED" "OR4K5 WILD-TYPE" "OR4K5 WILD-TYPE" 
     TCGA-GN-A266 
"OR4K5 WILD-TYPE" 
[1] "hr=" "1.6"
D18V2, continuous
                 vv
clus              DISTANT METASTASIS
  OR4K5 MUTATED                    4
  OR4K5 WILD-TYPE                  3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  OR4K5 MUTATED                                                                                          1
  OR4K5 WILD-TYPE                                                                                        4
                 vv
clus              REGIONAL LYMPH NODE
  OR4K5 MUTATED                     3
  OR4K5 WILD-TYPE                  10
D18V3, multiclass
                                                                                          clus
vv                                                                                         OR4K5 MUTATED
  DISTANT METASTASIS                                                                                   4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         OR4K5 WILD-TYPE
  DISTANT METASTASIS                                                                                     3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                   10
D18V4, binary
                 cls
clus               0  1
  OR4K5 MUTATED    2  6
  OR4K5 WILD-TYPE  6 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4K5 MUTATED      2    6
  OR4K5 WILD-TYPE    6   11
        clus
vv       OR4K5 MUTATED OR4K5 WILD-TYPE
  FEMALE             2               6
  MALE               6              11
                 vv
clus              N0 N1B N2C N3
  OR4K5 MUTATED    4   3   0  1
  OR4K5 WILD-TYPE 12   0   2  1
D18V5, multiclass
     clus
vv    OR4K5 MUTATED OR4K5 WILD-TYPE
  N0              4              12
  N1B             3               0
  N2C             0               2
  N3              1               1
D18V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  OR4K5 MUTATED          1        0        2         1          1          3
  OR4K5 WILD-TYPE        2        1        4         2          2          1
                 vv
clus              STAGE IV
  OR4K5 MUTATED          0
  OR4K5 WILD-TYPE        1
D18V7, multiclass

Clustering(19) Variable = SLC9A11 MUTATION ANALYSIS
D19V1, survival
                   sevent
clus2               0 1
  SLC9A11 MUTATED   1 3
  SLC9A11 WILD-TYPE 2 7
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
                4                 9 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
                3                 7 
$`SLC9A11 MUTATED`
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A2A2 TCGA-GN-A266 
        6.64        11.57        23.90        10.09 

$`SLC9A11 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
       30.87        10.03         1.12         1.35         1.08         9.47 
TCGA-EE-A29V TCGA-ER-A19F TCGA-FW-A3I3 
        2.43        11.11         0.20 

  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
             6.64              0.20 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
            23.90             30.87 
  SLC9A11 MUTATED SLC9A11 WILD-TYPE 
            10.83              2.43 
[1] "6.6 - 23.9 (10.8)" "0.2 - 30.9 (2.4)" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE"   "SLC9A11 MUTATED"   "SLC9A11 MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"SLC9A11 WILD-TYPE"   "SLC9A11 MUTATED" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-GN-A266 
  "SLC9A11 MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE"   "SLC9A11 MUTATED"   "SLC9A11 MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"SLC9A11 WILD-TYPE"   "SLC9A11 MUTATED" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-GN-A266 
  "SLC9A11 MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE"   "SLC9A11 MUTATED"   "SLC9A11 MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"SLC9A11 WILD-TYPE"   "SLC9A11 MUTATED" "SLC9A11 WILD-TYPE" "SLC9A11 WILD-TYPE" 
       TCGA-GN-A266 
  "SLC9A11 MUTATED" 
[1] "hr=" "2.2"
D19V2, continuous
                   vv
clus                DISTANT METASTASIS
  SLC9A11 MUTATED                    2
  SLC9A11 WILD-TYPE                  5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  SLC9A11 MUTATED                                                                                          4
  SLC9A11 WILD-TYPE                                                                                        1
                   vv
clus                REGIONAL LYMPH NODE
  SLC9A11 MUTATED                     5
  SLC9A11 WILD-TYPE                   8
D19V3, multiclass
                                                                                          clus
vv                                                                                         SLC9A11 MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         SLC9A11 WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 1
  REGIONAL LYMPH NODE                                                                                      8
D19V4, binary
                   cls
clus                 0  1
  SLC9A11 MUTATED    4  7
  SLC9A11 WILD-TYPE  4 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A11 MUTATED      4    7
  SLC9A11 WILD-TYPE    4   10
        clus
vv       SLC9A11 MUTATED SLC9A11 WILD-TYPE
  FEMALE               4                 4
  MALE                 7                10
                   vv
clus                N0 N1B N2C N3
  SLC9A11 MUTATED    7   1   1  0
  SLC9A11 WILD-TYPE  9   2   1  2
D19V5, multiclass
     clus
vv    SLC9A11 MUTATED SLC9A11 WILD-TYPE
  N0                7                 9
  N1B               1                 2
  N2C               1                 1
  N3                0                 2
D19V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  SLC9A11 MUTATED          2        0        3         2          2          0
  SLC9A11 WILD-TYPE        1        1        3         1          1          4
                   vv
clus                STAGE IV
  SLC9A11 MUTATED          0
  SLC9A11 WILD-TYPE        1
D19V7, multiclass

Clustering(20) Variable = ADAMTS20 MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                0 1
  ADAMTS20 MUTATED   2 6
  ADAMTS20 WILD-TYPE 1 4
  ADAMTS20 MUTATED ADAMTS20 WILD-TYPE 
                 8                  5 
  ADAMTS20 MUTATED ADAMTS20 WILD-TYPE 
                 6                  4 
$`ADAMTS20 MUTATED`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29V 
       30.87         6.64         1.12         1.35         1.08         2.43 
TCGA-EE-A2A2 TCGA-GN-A266 
       23.90        10.09 

$`ADAMTS20 WILD-TYPE`
TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A29N TCGA-ER-A19F TCGA-FW-A3I3 
       10.03        11.57         9.47        11.11         0.20 

  ADAMTS20 MUTATED ADAMTS20 WILD-TYPE 
              1.08               0.20 
  ADAMTS20 MUTATED ADAMTS20 WILD-TYPE 
             30.87              11.57 
  ADAMTS20 MUTATED ADAMTS20 WILD-TYPE 
             4.535             10.030 
[1] "1.1 - 30.9 (4.5)"  "0.2 - 11.6 (10.0)"
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "ADAMTS20 MUTATED" "ADAMTS20 WILD-TYPE"   "ADAMTS20 MUTATED" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"ADAMTS20 WILD-TYPE"   "ADAMTS20 MUTATED"   "ADAMTS20 MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "ADAMTS20 MUTATED" "ADAMTS20 WILD-TYPE"   "ADAMTS20 MUTATED" 
        TCGA-EE-A2A2         TCGA-ER-A19F         TCGA-FW-A3I3 
  "ADAMTS20 MUTATED" "ADAMTS20 WILD-TYPE" "ADAMTS20 WILD-TYPE" 
        TCGA-GN-A266 
  "ADAMTS20 MUTATED" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "ADAMTS20 MUTATED" "ADAMTS20 WILD-TYPE"   "ADAMTS20 MUTATED" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"ADAMTS20 WILD-TYPE"   "ADAMTS20 MUTATED"   "ADAMTS20 MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "ADAMTS20 MUTATED" "ADAMTS20 WILD-TYPE"   "ADAMTS20 MUTATED" 
        TCGA-EE-A2A2         TCGA-ER-A19F         TCGA-FW-A3I3 
  "ADAMTS20 MUTATED" "ADAMTS20 WILD-TYPE" "ADAMTS20 WILD-TYPE" 
        TCGA-GN-A266 
  "ADAMTS20 MUTATED" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "ADAMTS20 MUTATED" "ADAMTS20 WILD-TYPE"   "ADAMTS20 MUTATED" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"ADAMTS20 WILD-TYPE"   "ADAMTS20 MUTATED"   "ADAMTS20 MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "ADAMTS20 MUTATED" "ADAMTS20 WILD-TYPE"   "ADAMTS20 MUTATED" 
        TCGA-EE-A2A2         TCGA-ER-A19F         TCGA-FW-A3I3 
  "ADAMTS20 MUTATED" "ADAMTS20 WILD-TYPE" "ADAMTS20 WILD-TYPE" 
        TCGA-GN-A266 
  "ADAMTS20 MUTATED" 
[1] "hr=" "1.2"
D20V2, continuous
                    vv
clus                 DISTANT METASTASIS
  ADAMTS20 MUTATED                    6
  ADAMTS20 WILD-TYPE                  1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ADAMTS20 MUTATED                                                                                          3
  ADAMTS20 WILD-TYPE                                                                                        2
                    vv
clus                 REGIONAL LYMPH NODE
  ADAMTS20 MUTATED                     6
  ADAMTS20 WILD-TYPE                   7
D20V3, multiclass
                                                                                          clus
vv                                                                                         ADAMTS20 MUTATED
  DISTANT METASTASIS                                                                                      6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     6
                                                                                          clus
vv                                                                                         ADAMTS20 WILD-TYPE
  DISTANT METASTASIS                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  2
  REGIONAL LYMPH NODE                                                                                       7
D20V4, binary
                    cls
clus                  0  1
  ADAMTS20 MUTATED    5 10
  ADAMTS20 WILD-TYPE  3  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS20 MUTATED      5   10
  ADAMTS20 WILD-TYPE    3    7
        clus
vv       ADAMTS20 MUTATED ADAMTS20 WILD-TYPE
  FEMALE                5                  3
  MALE                 10                  7
                    vv
clus                 N0 N1B N2C N3
  ADAMTS20 MUTATED    7   3   2  1
  ADAMTS20 WILD-TYPE  9   0   0  1
D20V5, multiclass
     clus
vv    ADAMTS20 MUTATED ADAMTS20 WILD-TYPE
  N0                 7                  9
  N1B                3                  0
  N2C                2                  0
  N3                 1                  1
D20V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  ADAMTS20 MUTATED          1        1        3         2          3          3
  ADAMTS20 WILD-TYPE        2        0        3         1          0          1
                    vv
clus                 STAGE IV
  ADAMTS20 MUTATED          0
  ADAMTS20 WILD-TYPE        1
D20V7, multiclass

Clustering(21) Variable = SLC38A4 MUTATION ANALYSIS
D21V1, survival
                   sevent
clus2               0 1
  SLC38A4 MUTATED   2 3
  SLC38A4 WILD-TYPE 1 7
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
                5                 8 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
                3                 7 
$`SLC38A4 MUTATED`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A2A2 TCGA-GN-A266 
       30.87         6.64         1.12        23.90        10.09 

$`SLC38A4 WILD-TYPE`
TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V 
       10.03        11.57         1.35         1.08         9.47         2.43 
TCGA-ER-A19F TCGA-FW-A3I3 
       11.11         0.20 

  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
             1.12              0.20 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
            30.87             11.57 
  SLC38A4 MUTATED SLC38A4 WILD-TYPE 
            10.09              5.95 
[1] "1.1 - 30.9 (10.1)" "0.2 - 11.6 (6.0)" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "SLC38A4 MUTATED" "SLC38A4 WILD-TYPE"   "SLC38A4 MUTATED" "SLC38A4 WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "SLC38A4 MUTATED" "SLC38A4 WILD-TYPE" "SLC38A4 WILD-TYPE" "SLC38A4 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"SLC38A4 WILD-TYPE"   "SLC38A4 MUTATED" "SLC38A4 WILD-TYPE" "SLC38A4 WILD-TYPE" 
       TCGA-GN-A266 
  "SLC38A4 MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "SLC38A4 MUTATED" "SLC38A4 WILD-TYPE"   "SLC38A4 MUTATED" "SLC38A4 WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "SLC38A4 MUTATED" "SLC38A4 WILD-TYPE" "SLC38A4 WILD-TYPE" "SLC38A4 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"SLC38A4 WILD-TYPE"   "SLC38A4 MUTATED" "SLC38A4 WILD-TYPE" "SLC38A4 WILD-TYPE" 
       TCGA-GN-A266 
  "SLC38A4 MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "SLC38A4 MUTATED" "SLC38A4 WILD-TYPE"   "SLC38A4 MUTATED" "SLC38A4 WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "SLC38A4 MUTATED" "SLC38A4 WILD-TYPE" "SLC38A4 WILD-TYPE" "SLC38A4 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"SLC38A4 WILD-TYPE"   "SLC38A4 MUTATED" "SLC38A4 WILD-TYPE" "SLC38A4 WILD-TYPE" 
       TCGA-GN-A266 
  "SLC38A4 MUTATED" 
[1] "hr=" "2.3"
D21V2, continuous
                   vv
clus                DISTANT METASTASIS
  SLC38A4 MUTATED                    1
  SLC38A4 WILD-TYPE                  6
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  SLC38A4 MUTATED                                                                                          2
  SLC38A4 WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  SLC38A4 MUTATED                     6
  SLC38A4 WILD-TYPE                   7
D21V3, multiclass
                                                                                          clus
vv                                                                                         SLC38A4 MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    6
                                                                                          clus
vv                                                                                         SLC38A4 WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                      7
D21V4, binary
                   cls
clus                0 1
  SLC38A4 MUTATED   1 8
  SLC38A4 WILD-TYPE 7 9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A4 MUTATED      1    8
  SLC38A4 WILD-TYPE    7    9
        clus
vv       SLC38A4 MUTATED SLC38A4 WILD-TYPE
  FEMALE               1                 7
  MALE                 8                 9
                   vv
clus                N0 N1B N2C N3
  SLC38A4 MUTATED    6   1   1  0
  SLC38A4 WILD-TYPE 10   2   1  2
D21V5, multiclass
     clus
vv    SLC38A4 MUTATED SLC38A4 WILD-TYPE
  N0                6                10
  N1B               1                 2
  N2C               1                 1
  N3                0                 2
D21V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  SLC38A4 MUTATED          1        1        3         1          2          0
  SLC38A4 WILD-TYPE        2        0        3         2          1          4
                   vv
clus                STAGE IV
  SLC38A4 MUTATED          0
  SLC38A4 WILD-TYPE        1
D21V7, multiclass

Clustering(22) Variable = OR2T2 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2             0 1
  OR2T2 MUTATED   0 3
  OR2T2 WILD-TYPE 3 7
  OR2T2 MUTATED OR2T2 WILD-TYPE 
              3              10 
  OR2T2 MUTATED OR2T2 WILD-TYPE 
              3               7 
$`OR2T2 MUTATED`
TCGA-DA-A1IC TCGA-EE-A182 TCGA-GN-A266 
        6.64         1.35        10.09 

$`OR2T2 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29N 
       30.87        10.03        11.57         1.12         1.08         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 
        2.43        23.90        11.11         0.20 

  OR2T2 MUTATED OR2T2 WILD-TYPE 
           1.35            0.20 
  OR2T2 MUTATED OR2T2 WILD-TYPE 
          10.09           30.87 
  OR2T2 MUTATED OR2T2 WILD-TYPE 
           6.64            9.75 
[1] "1.4 - 10.1 (6.6)" "0.2 - 30.9 (9.8)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"OR2T2 WILD-TYPE" "OR2T2 WILD-TYPE"   "OR2T2 MUTATED" "OR2T2 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"OR2T2 WILD-TYPE"   "OR2T2 MUTATED" "OR2T2 WILD-TYPE" "OR2T2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"OR2T2 WILD-TYPE" "OR2T2 WILD-TYPE" "OR2T2 WILD-TYPE" "OR2T2 WILD-TYPE" 
     TCGA-GN-A266 
  "OR2T2 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"OR2T2 WILD-TYPE" "OR2T2 WILD-TYPE"   "OR2T2 MUTATED" "OR2T2 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"OR2T2 WILD-TYPE"   "OR2T2 MUTATED" "OR2T2 WILD-TYPE" "OR2T2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"OR2T2 WILD-TYPE" "OR2T2 WILD-TYPE" "OR2T2 WILD-TYPE" "OR2T2 WILD-TYPE" 
     TCGA-GN-A266 
  "OR2T2 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"OR2T2 WILD-TYPE" "OR2T2 WILD-TYPE"   "OR2T2 MUTATED" "OR2T2 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"OR2T2 WILD-TYPE"   "OR2T2 MUTATED" "OR2T2 WILD-TYPE" "OR2T2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"OR2T2 WILD-TYPE" "OR2T2 WILD-TYPE" "OR2T2 WILD-TYPE" "OR2T2 WILD-TYPE" 
     TCGA-GN-A266 
  "OR2T2 MUTATED" 
[1] "hr=" "2.1"
D22V2, continuous
                 vv
clus              DISTANT METASTASIS
  OR2T2 MUTATED                    1
  OR2T2 WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  OR2T2 MUTATED                                                                                          2
  OR2T2 WILD-TYPE                                                                                        3
                 vv
clus              REGIONAL LYMPH NODE
  OR2T2 MUTATED                     2
  OR2T2 WILD-TYPE                  11
D22V3, multiclass
                                                                                          clus
vv                                                                                         OR2T2 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  2
                                                                                          clus
vv                                                                                         OR2T2 WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                   11
D22V4, binary
                 cls
clus               0  1
  OR2T2 MUTATED    1  4
  OR2T2 WILD-TYPE  7 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T2 MUTATED      1    4
  OR2T2 WILD-TYPE    7   13
        clus
vv       OR2T2 MUTATED OR2T2 WILD-TYPE
  FEMALE             1               7
  MALE               4              13
                 vv
clus              N0 N1B N2C N3
  OR2T2 MUTATED    2   1   1  0
  OR2T2 WILD-TYPE 14   2   1  2
D22V5, multiclass
     clus
vv    OR2T2 MUTATED OR2T2 WILD-TYPE
  N0              2              14
  N1B             1               2
  N2C             1               1
  N3              0               2
D22V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  OR2T2 MUTATED          0        0        1         1          1          1
  OR2T2 WILD-TYPE        3        1        5         2          2          3
                 vv
clus              STAGE IV
  OR2T2 MUTATED          0
  OR2T2 WILD-TYPE        1
D22V7, multiclass

Clustering(23) Variable = PRB2 MUTATION ANALYSIS
D23V1, survival
                sevent
clus2            0 1
  PRB2 MUTATED   1 3
  PRB2 WILD-TYPE 2 7
  PRB2 MUTATED PRB2 WILD-TYPE 
             4              9 
  PRB2 MUTATED PRB2 WILD-TYPE 
             3              7 
$`PRB2 MUTATED`
TCGA-D3-A2JF TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A29V 
       30.87         1.12         9.47         2.43 

$`PRB2 WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A2A2 
       10.03         6.64        11.57         1.35         1.08        23.90 
TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
       11.11         0.20        10.09 

  PRB2 MUTATED PRB2 WILD-TYPE 
          1.12           0.20 
  PRB2 MUTATED PRB2 WILD-TYPE 
         30.87          23.90 
  PRB2 MUTATED PRB2 WILD-TYPE 
          5.95          10.03 
[1] "1.1 - 30.9 (6.0)"  "0.2 - 23.9 (10.0)"
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
  "PRB2 MUTATED" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "PRB2 MUTATED" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE"   "PRB2 MUTATED" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
  "PRB2 MUTATED" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-GN-A266 
"PRB2 WILD-TYPE" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
  "PRB2 MUTATED" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "PRB2 MUTATED" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE"   "PRB2 MUTATED" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
  "PRB2 MUTATED" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-GN-A266 
"PRB2 WILD-TYPE" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
  "PRB2 MUTATED" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "PRB2 MUTATED" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE"   "PRB2 MUTATED" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
  "PRB2 MUTATED" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-GN-A266 
"PRB2 WILD-TYPE" 
[1] "hr=" "1.1"
D23V2, continuous
                vv
clus             DISTANT METASTASIS
  PRB2 MUTATED                    3
  PRB2 WILD-TYPE                  4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  PRB2 MUTATED                                                                                          1
  PRB2 WILD-TYPE                                                                                        4
                vv
clus             REGIONAL LYMPH NODE
  PRB2 MUTATED                     5
  PRB2 WILD-TYPE                   8
D23V3, multiclass
                                                                                          clus
vv                                                                                         PRB2 MUTATED
  DISTANT METASTASIS                                                                                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            1
  REGIONAL LYMPH NODE                                                                                 5
                                                                                          clus
vv                                                                                         PRB2 WILD-TYPE
  DISTANT METASTASIS                                                                                    4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              4
  REGIONAL LYMPH NODE                                                                                   8
D23V4, binary
                cls
clus              0  1
  PRB2 MUTATED    3  6
  PRB2 WILD-TYPE  5 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      3    6
  PRB2 WILD-TYPE    5   11
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  FEMALE            3              5
  MALE              6             11
                vv
clus             N0 N1B N2C N3
  PRB2 MUTATED    7   1   1  0
  PRB2 WILD-TYPE  9   2   1  2
D23V5, multiclass
     clus
vv    PRB2 MUTATED PRB2 WILD-TYPE
  N0             7              9
  N1B            1              2
  N2C            1              1
  N3             0              2
D23V6, continuous
                vv
clus             STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  PRB2 MUTATED          2        0        3         1          1          1
  PRB2 WILD-TYPE        1        1        3         2          2          3
                vv
clus             STAGE IV
  PRB2 MUTATED          0
  PRB2 WILD-TYPE        1
D23V7, multiclass

Clustering(24) Variable = COL21A1 MUTATION ANALYSIS
D24V1, survival
                   sevent
clus2               0 1
  COL21A1 MUTATED   2 5
  COL21A1 WILD-TYPE 1 5
  COL21A1 MUTATED COL21A1 WILD-TYPE 
                7                 6 
  COL21A1 MUTATED COL21A1 WILD-TYPE 
                5                 5 
$`COL21A1 MUTATED`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A2A2 TCGA-ER-A19F 
       30.87        10.03        11.57         1.12        23.90        11.11 
TCGA-GN-A266 
       10.09 

$`COL21A1 WILD-TYPE`
TCGA-DA-A1IC TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V TCGA-FW-A3I3 
        6.64         1.35         1.08         9.47         2.43         0.20 

  COL21A1 MUTATED COL21A1 WILD-TYPE 
             1.12              0.20 
  COL21A1 MUTATED COL21A1 WILD-TYPE 
            30.87              9.47 
  COL21A1 MUTATED COL21A1 WILD-TYPE 
            11.11              1.89 
[1] "1.1 - 30.9 (11.1)" "0.2 - 9.5 (1.9)"  
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "COL21A1 MUTATED"   "COL21A1 MUTATED" "COL21A1 WILD-TYPE"   "COL21A1 MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "COL21A1 MUTATED" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"COL21A1 WILD-TYPE"   "COL21A1 MUTATED"   "COL21A1 MUTATED" "COL21A1 WILD-TYPE" 
       TCGA-GN-A266 
  "COL21A1 MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "COL21A1 MUTATED"   "COL21A1 MUTATED" "COL21A1 WILD-TYPE"   "COL21A1 MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "COL21A1 MUTATED" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"COL21A1 WILD-TYPE"   "COL21A1 MUTATED"   "COL21A1 MUTATED" "COL21A1 WILD-TYPE" 
       TCGA-GN-A266 
  "COL21A1 MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "COL21A1 MUTATED"   "COL21A1 MUTATED" "COL21A1 WILD-TYPE"   "COL21A1 MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "COL21A1 MUTATED" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"COL21A1 WILD-TYPE"   "COL21A1 MUTATED"   "COL21A1 MUTATED" "COL21A1 WILD-TYPE" 
       TCGA-GN-A266 
  "COL21A1 MUTATED" 
[1] "hr=" "12" 
D24V2, continuous
                   vv
clus                DISTANT METASTASIS
  COL21A1 MUTATED                    1
  COL21A1 WILD-TYPE                  6
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  COL21A1 MUTATED                                                                                          3
  COL21A1 WILD-TYPE                                                                                        2
                   vv
clus                REGIONAL LYMPH NODE
  COL21A1 MUTATED                     6
  COL21A1 WILD-TYPE                   7
D24V3, multiclass
                                                                                          clus
vv                                                                                         COL21A1 MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    6
                                                                                          clus
vv                                                                                         COL21A1 WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 2
  REGIONAL LYMPH NODE                                                                                      7
D24V4, binary
                   cls
clus                0 1
  COL21A1 MUTATED   1 9
  COL21A1 WILD-TYPE 7 8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL21A1 MUTATED      1    9
  COL21A1 WILD-TYPE    7    8
        clus
vv       COL21A1 MUTATED COL21A1 WILD-TYPE
  FEMALE               1                 7
  MALE                 9                 8
                   vv
clus                N0 N1B N2C N3
  COL21A1 MUTATED    7   1   0  1
  COL21A1 WILD-TYPE  9   2   2  1
D24V5, multiclass
     clus
vv    COL21A1 MUTATED COL21A1 WILD-TYPE
  N0                7                 9
  N1B               1                 2
  N2C               0                 2
  N3                1                 1
D24V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  COL21A1 MUTATED          2        1        3         0          1          1
  COL21A1 WILD-TYPE        1        0        3         3          2          3
                   vv
clus                STAGE IV
  COL21A1 MUTATED          0
  COL21A1 WILD-TYPE        1
D24V7, multiclass

Clustering(25) Variable = OR4N2 MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2             0 1
  OR4N2 MUTATED   1 4
  OR4N2 WILD-TYPE 2 6
  OR4N2 MUTATED OR4N2 WILD-TYPE 
              5               8 
  OR4N2 MUTATED OR4N2 WILD-TYPE 
              4               6 
$`OR4N2 MUTATED`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A29V TCGA-ER-A19F TCGA-GN-A266 
       30.87        10.03         2.43        11.11        10.09 

$`OR4N2 WILD-TYPE`
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
        6.64        11.57         1.12         1.35         1.08         9.47 
TCGA-EE-A2A2 TCGA-FW-A3I3 
       23.90         0.20 

  OR4N2 MUTATED OR4N2 WILD-TYPE 
           2.43            0.20 
  OR4N2 MUTATED OR4N2 WILD-TYPE 
          30.87           23.90 
  OR4N2 MUTATED OR4N2 WILD-TYPE 
         10.090           3.995 
[1] "2.4 - 30.9 (10.1)" "0.2 - 23.9 (4.0)" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "OR4N2 MUTATED"   "OR4N2 MUTATED" "OR4N2 WILD-TYPE" "OR4N2 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"OR4N2 WILD-TYPE" "OR4N2 WILD-TYPE" "OR4N2 WILD-TYPE" "OR4N2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "OR4N2 MUTATED" "OR4N2 WILD-TYPE"   "OR4N2 MUTATED" "OR4N2 WILD-TYPE" 
     TCGA-GN-A266 
  "OR4N2 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "OR4N2 MUTATED"   "OR4N2 MUTATED" "OR4N2 WILD-TYPE" "OR4N2 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"OR4N2 WILD-TYPE" "OR4N2 WILD-TYPE" "OR4N2 WILD-TYPE" "OR4N2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "OR4N2 MUTATED" "OR4N2 WILD-TYPE"   "OR4N2 MUTATED" "OR4N2 WILD-TYPE" 
     TCGA-GN-A266 
  "OR4N2 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "OR4N2 MUTATED"   "OR4N2 MUTATED" "OR4N2 WILD-TYPE" "OR4N2 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"OR4N2 WILD-TYPE" "OR4N2 WILD-TYPE" "OR4N2 WILD-TYPE" "OR4N2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "OR4N2 MUTATED" "OR4N2 WILD-TYPE"   "OR4N2 MUTATED" "OR4N2 WILD-TYPE" 
     TCGA-GN-A266 
  "OR4N2 MUTATED" 
[1] "hr=" "1.6"
D25V2, continuous
                 vv
clus              DISTANT METASTASIS
  OR4N2 MUTATED                    2
  OR4N2 WILD-TYPE                  5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  OR4N2 MUTATED                                                                                          3
  OR4N2 WILD-TYPE                                                                                        2
                 vv
clus              REGIONAL LYMPH NODE
  OR4N2 MUTATED                     4
  OR4N2 WILD-TYPE                   9
D25V3, multiclass
                                                                                          clus
vv                                                                                         OR4N2 MUTATED
  DISTANT METASTASIS                                                                                   2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             3
  REGIONAL LYMPH NODE                                                                                  4
                                                                                          clus
vv                                                                                         OR4N2 WILD-TYPE
  DISTANT METASTASIS                                                                                     5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    9
D25V4, binary
                 cls
clus              0 1
  OR4N2 MUTATED   0 9
  OR4N2 WILD-TYPE 8 8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N2 MUTATED      0    9
  OR4N2 WILD-TYPE    8    8
        clus
vv       OR4N2 MUTATED OR4N2 WILD-TYPE
  FEMALE             0               8
  MALE               9               8
                 vv
clus              N0 N1B N2C N3
  OR4N2 MUTATED    6   1   0  1
  OR4N2 WILD-TYPE 10   2   2  1
D25V5, multiclass
     clus
vv    OR4N2 MUTATED OR4N2 WILD-TYPE
  N0              6              10
  N1B             1               2
  N2C             0               2
  N3              1               1
D25V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  OR4N2 MUTATED          1        1        2         1          0          2
  OR4N2 WILD-TYPE        2        0        4         2          3          2
                 vv
clus              STAGE IV
  OR4N2 MUTATED          0
  OR4N2 WILD-TYPE        1
D25V7, multiclass

Clustering(26) Variable = PROX1 MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2             0 1
  PROX1 MUTATED   1 2
  PROX1 WILD-TYPE 2 8
  PROX1 MUTATED PROX1 WILD-TYPE 
              3              10 
  PROX1 MUTATED PROX1 WILD-TYPE 
              2               8 
$`PROX1 MUTATED`
TCGA-EE-A181 TCGA-EE-A29V TCGA-EE-A2A2 
        1.12         2.43        23.90 

$`PROX1 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L 
       30.87        10.03         6.64        11.57         1.35         1.08 
TCGA-EE-A29N TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        9.47        11.11         0.20        10.09 

  PROX1 MUTATED PROX1 WILD-TYPE 
           1.12            0.20 
  PROX1 MUTATED PROX1 WILD-TYPE 
          23.90           30.87 
  PROX1 MUTATED PROX1 WILD-TYPE 
           2.43            9.75 
[1] "1.1 - 23.9 (2.4)" "0.2 - 30.9 (9.8)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "PROX1 MUTATED" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "PROX1 MUTATED"   "PROX1 MUTATED" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-GN-A266 
"PROX1 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "PROX1 MUTATED" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "PROX1 MUTATED"   "PROX1 MUTATED" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-GN-A266 
"PROX1 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "PROX1 MUTATED" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "PROX1 MUTATED"   "PROX1 MUTATED" "PROX1 WILD-TYPE" "PROX1 WILD-TYPE" 
     TCGA-GN-A266 
"PROX1 WILD-TYPE" 
[1] "hr=" "1.1"
D26V2, continuous
                 vv
clus              DISTANT METASTASIS
  PROX1 MUTATED                    1
  PROX1 WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  PROX1 MUTATED                                                                                          0
  PROX1 WILD-TYPE                                                                                        5
                 vv
clus              REGIONAL LYMPH NODE
  PROX1 MUTATED                     5
  PROX1 WILD-TYPE                   8
D26V3, multiclass
                                                                                          clus
vv                                                                                         PROX1 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
  REGIONAL LYMPH NODE                                                                                  5
                                                                                          clus
vv                                                                                         PROX1 WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                    8
D26V4, binary
                 cls
clus               0  1
  PROX1 MUTATED    1  5
  PROX1 WILD-TYPE  7 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROX1 MUTATED      1    5
  PROX1 WILD-TYPE    7   12
        clus
vv       PROX1 MUTATED PROX1 WILD-TYPE
  FEMALE             1               7
  MALE               5              12
                 vv
clus              N0 N1B N2C N3
  PROX1 MUTATED    4   2   0  0
  PROX1 WILD-TYPE 12   1   2  2
D26V5, multiclass
     clus
vv    PROX1 MUTATED PROX1 WILD-TYPE
  N0              4              12
  N1B             2               1
  N2C             0               2
  N3              0               2
D26V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  PROX1 MUTATED          0        1        3         0          1          1
  PROX1 WILD-TYPE        3        0        3         3          2          3
                 vv
clus              STAGE IV
  PROX1 MUTATED          0
  PROX1 WILD-TYPE        1
D26V7, multiclass

Clustering(27) Variable = ANGPT1 MUTATION ANALYSIS
D27V1, survival
                  sevent
clus2              0 1
  ANGPT1 MUTATED   2 2
  ANGPT1 WILD-TYPE 1 8
  ANGPT1 MUTATED ANGPT1 WILD-TYPE 
               4                9 
  ANGPT1 MUTATED ANGPT1 WILD-TYPE 
               2                8 
$`ANGPT1 MUTATED`
TCGA-D3-A2JF TCGA-EE-A182 TCGA-EE-A2A2 TCGA-GN-A266 
       30.87         1.35        23.90        10.09 

$`ANGPT1 WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29N 
       10.03         6.64        11.57         1.12         1.08         9.47 
TCGA-EE-A29V TCGA-ER-A19F TCGA-FW-A3I3 
        2.43        11.11         0.20 

  ANGPT1 MUTATED ANGPT1 WILD-TYPE 
            1.35             0.20 
  ANGPT1 MUTATED ANGPT1 WILD-TYPE 
           30.87            11.57 
  ANGPT1 MUTATED ANGPT1 WILD-TYPE 
          16.995            6.640 
[1] "1.4 - 30.9 (17.0)" "0.2 - 11.6 (6.6)" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
  "ANGPT1 MUTATED" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"ANGPT1 WILD-TYPE"   "ANGPT1 MUTATED" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"ANGPT1 WILD-TYPE"   "ANGPT1 MUTATED" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-GN-A266 
  "ANGPT1 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
  "ANGPT1 MUTATED" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"ANGPT1 WILD-TYPE"   "ANGPT1 MUTATED" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"ANGPT1 WILD-TYPE"   "ANGPT1 MUTATED" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-GN-A266 
  "ANGPT1 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
  "ANGPT1 MUTATED" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"ANGPT1 WILD-TYPE"   "ANGPT1 MUTATED" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"ANGPT1 WILD-TYPE"   "ANGPT1 MUTATED" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-GN-A266 
  "ANGPT1 MUTATED" 
[1] "hr=" "3.5"
D27V2, continuous
                  vv
clus               DISTANT METASTASIS
  ANGPT1 MUTATED                    3
  ANGPT1 WILD-TYPE                  4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ANGPT1 MUTATED                                                                                          3
  ANGPT1 WILD-TYPE                                                                                        2
                  vv
clus               REGIONAL LYMPH NODE
  ANGPT1 MUTATED                     3
  ANGPT1 WILD-TYPE                  10
D27V3, multiclass
                                                                                          clus
vv                                                                                         ANGPT1 MUTATED
  DISTANT METASTASIS                                                                                    3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              3
  REGIONAL LYMPH NODE                                                                                   3
                                                                                          clus
vv                                                                                         ANGPT1 WILD-TYPE
  DISTANT METASTASIS                                                                                      4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                    10
D27V4, binary
                  cls
clus                0  1
  ANGPT1 MUTATED    3  6
  ANGPT1 WILD-TYPE  5 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANGPT1 MUTATED      3    6
  ANGPT1 WILD-TYPE    5   11
        clus
vv       ANGPT1 MUTATED ANGPT1 WILD-TYPE
  FEMALE              3                5
  MALE                6               11
                  vv
clus               N0 N1B N2C N3
  ANGPT1 MUTATED    5   2   1  0
  ANGPT1 WILD-TYPE 11   1   1  2
D27V5, multiclass
     clus
vv    ANGPT1 MUTATED ANGPT1 WILD-TYPE
  N0               5               11
  N1B              2                1
  N2C              1                1
  N3               0                2
D27V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  ANGPT1 MUTATED          1        0        2         2          2          1
  ANGPT1 WILD-TYPE        2        1        4         1          1          3
                  vv
clus               STAGE IV
  ANGPT1 MUTATED          0
  ANGPT1 WILD-TYPE        1
D27V7, multiclass

Clustering(28) Variable = C8A MUTATION ANALYSIS
D28V1, survival
               sevent
clus2           0 1
  C8A MUTATED   1 6
  C8A WILD-TYPE 2 4
  C8A MUTATED C8A WILD-TYPE 
            7             6 
  C8A MUTATED C8A WILD-TYPE 
            6             4 
$`C8A MUTATED`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A2A2 TCGA-ER-A19F 
       10.03         6.64         1.12         1.08        23.90        11.11 
TCGA-GN-A266 
       10.09 

$`C8A WILD-TYPE`
TCGA-D3-A2JF TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29N TCGA-EE-A29V TCGA-FW-A3I3 
       30.87        11.57         1.35         9.47         2.43         0.20 

  C8A MUTATED C8A WILD-TYPE 
         1.08          0.20 
  C8A MUTATED C8A WILD-TYPE 
        23.90         30.87 
  C8A MUTATED C8A WILD-TYPE 
        10.03          5.95 
[1] "1.1 - 23.9 (10.0)" "0.2 - 30.9 (6.0)" 
   TCGA-D3-A2JF    TCGA-DA-A1I0    TCGA-DA-A1IC    TCGA-EE-A17X    TCGA-EE-A181 
"C8A WILD-TYPE"   "C8A MUTATED"   "C8A MUTATED" "C8A WILD-TYPE"   "C8A MUTATED" 
   TCGA-EE-A182    TCGA-EE-A29L    TCGA-EE-A29N    TCGA-EE-A29V    TCGA-EE-A2A2 
"C8A WILD-TYPE"   "C8A MUTATED" "C8A WILD-TYPE" "C8A WILD-TYPE"   "C8A MUTATED" 
   TCGA-ER-A19F    TCGA-FW-A3I3    TCGA-GN-A266 
  "C8A MUTATED" "C8A WILD-TYPE"   "C8A MUTATED" 
   TCGA-D3-A2JF    TCGA-DA-A1I0    TCGA-DA-A1IC    TCGA-EE-A17X    TCGA-EE-A181 
"C8A WILD-TYPE"   "C8A MUTATED"   "C8A MUTATED" "C8A WILD-TYPE"   "C8A MUTATED" 
   TCGA-EE-A182    TCGA-EE-A29L    TCGA-EE-A29N    TCGA-EE-A29V    TCGA-EE-A2A2 
"C8A WILD-TYPE"   "C8A MUTATED" "C8A WILD-TYPE" "C8A WILD-TYPE"   "C8A MUTATED" 
   TCGA-ER-A19F    TCGA-FW-A3I3    TCGA-GN-A266 
  "C8A MUTATED" "C8A WILD-TYPE"   "C8A MUTATED" 
   TCGA-D3-A2JF    TCGA-DA-A1I0    TCGA-DA-A1IC    TCGA-EE-A17X    TCGA-EE-A181 
"C8A WILD-TYPE"   "C8A MUTATED"   "C8A MUTATED" "C8A WILD-TYPE"   "C8A MUTATED" 
   TCGA-EE-A182    TCGA-EE-A29L    TCGA-EE-A29N    TCGA-EE-A29V    TCGA-EE-A2A2 
"C8A WILD-TYPE"   "C8A MUTATED" "C8A WILD-TYPE" "C8A WILD-TYPE"   "C8A MUTATED" 
   TCGA-ER-A19F    TCGA-FW-A3I3    TCGA-GN-A266 
  "C8A MUTATED" "C8A WILD-TYPE"   "C8A MUTATED" 
[1] "hr=" "1.2"
D28V2, continuous
               vv
clus            DISTANT METASTASIS
  C8A MUTATED                    0
  C8A WILD-TYPE                  7
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  C8A MUTATED                                                                                          3
  C8A WILD-TYPE                                                                                        2
               vv
clus            REGIONAL LYMPH NODE
  C8A MUTATED                     5
  C8A WILD-TYPE                   8
D28V3, multiclass
                                                                                          clus
vv                                                                                         C8A MUTATED
  DISTANT METASTASIS                                                                                 0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)           3
  REGIONAL LYMPH NODE                                                                                5
                                                                                          clus
vv                                                                                         C8A WILD-TYPE
  DISTANT METASTASIS                                                                                   7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  8
D28V4, binary
               cls
clus             0  1
  C8A MUTATED    1  7
  C8A WILD-TYPE  7 10
[1] "tbl2"
               cls
clus            [,1] [,2]
  C8A MUTATED      1    7
  C8A WILD-TYPE    7   10
        clus
vv       C8A MUTATED C8A WILD-TYPE
  FEMALE           1             7
  MALE             7            10
               vv
clus            N0 N1B N2C N3
  C8A MUTATED    3   1   1  2
  C8A WILD-TYPE 13   2   1  0
D28V5, multiclass
     clus
vv    C8A MUTATED C8A WILD-TYPE
  N0            3            13
  N1B           1             2
  N2C           1             1
  N3            2             0
D28V6, continuous
               vv
clus            STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  C8A MUTATED          0        0        1         1          2          2
  C8A WILD-TYPE        3        1        5         2          1          2
               vv
clus            STAGE IV
  C8A MUTATED          0
  C8A WILD-TYPE        1
D28V7, multiclass

Clustering(29) Variable = SERPINB11 MUTATION ANALYSIS
D29V1, survival
                     sevent
clus2                 0 1
  SERPINB11 MUTATED   0 3
  SERPINB11 WILD-TYPE 3 7
  SERPINB11 MUTATED SERPINB11 WILD-TYPE 
                  3                  10 
  SERPINB11 MUTATED SERPINB11 WILD-TYPE 
                  3                   7 
$`SERPINB11 MUTATED`
TCGA-DA-A1I0 TCGA-EE-A182 TCGA-ER-A19F 
       10.03         1.35        11.11 

$`SERPINB11 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29N 
       30.87         6.64        11.57         1.12         1.08         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-FW-A3I3 TCGA-GN-A266 
        2.43        23.90         0.20        10.09 

  SERPINB11 MUTATED SERPINB11 WILD-TYPE 
               1.35                0.20 
  SERPINB11 MUTATED SERPINB11 WILD-TYPE 
              11.11               30.87 
  SERPINB11 MUTATED SERPINB11 WILD-TYPE 
             10.030               8.055 
[1] "1.4 - 11.1 (10.0)" "0.2 - 30.9 (8.1)" 
         TCGA-D3-A2JF          TCGA-DA-A1I0          TCGA-DA-A1IC 
"SERPINB11 WILD-TYPE"   "SERPINB11 MUTATED" "SERPINB11 WILD-TYPE" 
         TCGA-EE-A17X          TCGA-EE-A181          TCGA-EE-A182 
"SERPINB11 WILD-TYPE" "SERPINB11 WILD-TYPE"   "SERPINB11 MUTATED" 
         TCGA-EE-A29L          TCGA-EE-A29N          TCGA-EE-A29V 
"SERPINB11 WILD-TYPE" "SERPINB11 WILD-TYPE" "SERPINB11 WILD-TYPE" 
         TCGA-EE-A2A2          TCGA-ER-A19F          TCGA-FW-A3I3 
"SERPINB11 WILD-TYPE"   "SERPINB11 MUTATED" "SERPINB11 WILD-TYPE" 
         TCGA-GN-A266 
"SERPINB11 WILD-TYPE" 
         TCGA-D3-A2JF          TCGA-DA-A1I0          TCGA-DA-A1IC 
"SERPINB11 WILD-TYPE"   "SERPINB11 MUTATED" "SERPINB11 WILD-TYPE" 
         TCGA-EE-A17X          TCGA-EE-A181          TCGA-EE-A182 
"SERPINB11 WILD-TYPE" "SERPINB11 WILD-TYPE"   "SERPINB11 MUTATED" 
         TCGA-EE-A29L          TCGA-EE-A29N          TCGA-EE-A29V 
"SERPINB11 WILD-TYPE" "SERPINB11 WILD-TYPE" "SERPINB11 WILD-TYPE" 
         TCGA-EE-A2A2          TCGA-ER-A19F          TCGA-FW-A3I3 
"SERPINB11 WILD-TYPE"   "SERPINB11 MUTATED" "SERPINB11 WILD-TYPE" 
         TCGA-GN-A266 
"SERPINB11 WILD-TYPE" 
         TCGA-D3-A2JF          TCGA-DA-A1I0          TCGA-DA-A1IC 
"SERPINB11 WILD-TYPE"   "SERPINB11 MUTATED" "SERPINB11 WILD-TYPE" 
         TCGA-EE-A17X          TCGA-EE-A181          TCGA-EE-A182 
"SERPINB11 WILD-TYPE" "SERPINB11 WILD-TYPE"   "SERPINB11 MUTATED" 
         TCGA-EE-A29L          TCGA-EE-A29N          TCGA-EE-A29V 
"SERPINB11 WILD-TYPE" "SERPINB11 WILD-TYPE" "SERPINB11 WILD-TYPE" 
         TCGA-EE-A2A2          TCGA-ER-A19F          TCGA-FW-A3I3 
"SERPINB11 WILD-TYPE"   "SERPINB11 MUTATED" "SERPINB11 WILD-TYPE" 
         TCGA-GN-A266 
"SERPINB11 WILD-TYPE" 
[1] "hr=" "1.4"
D29V2, continuous
                     vv
clus                  DISTANT METASTASIS
  SERPINB11 MUTATED                    1
  SERPINB11 WILD-TYPE                  6
                     vv
clus                  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  SERPINB11 MUTATED                                                                                          2
  SERPINB11 WILD-TYPE                                                                                        3
                     vv
clus                  REGIONAL LYMPH NODE
  SERPINB11 MUTATED                     4
  SERPINB11 WILD-TYPE                   9
D29V3, multiclass
                                                                                          clus
vv                                                                                         SERPINB11 MUTATED
  DISTANT METASTASIS                                                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 2
  REGIONAL LYMPH NODE                                                                                      4
                                                                                          clus
vv                                                                                         SERPINB11 WILD-TYPE
  DISTANT METASTASIS                                                                                         6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                   3
  REGIONAL LYMPH NODE                                                                                        9
D29V4, binary
                     cls
clus                   0  1
  SERPINB11 MUTATED    2  5
  SERPINB11 WILD-TYPE  6 12
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB11 MUTATED      2    5
  SERPINB11 WILD-TYPE    6   12
        clus
vv       SERPINB11 MUTATED SERPINB11 WILD-TYPE
  FEMALE                 2                   6
  MALE                   5                  12
                     vv
clus                  N0 N1B N2C N3
  SERPINB11 MUTATED    5   1   0  1
  SERPINB11 WILD-TYPE 11   2   2  1
D29V5, multiclass
     clus
vv    SERPINB11 MUTATED SERPINB11 WILD-TYPE
  N0                  5                  11
  N1B                 1                   2
  N2C                 0                   2
  N3                  1                   1
D29V6, continuous
                     vv
clus                  STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB
  SERPINB11 MUTATED          0        1        2         1          0
  SERPINB11 WILD-TYPE        3        0        4         2          3
                     vv
clus                  STAGE IIIC STAGE IV
  SERPINB11 MUTATED            2        0
  SERPINB11 WILD-TYPE          2        1
D29V7, multiclass

Clustering(30) Variable = C18ORF34 MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                0 1
  C18ORF34 MUTATED   1 4
  C18ORF34 WILD-TYPE 2 6
  C18ORF34 MUTATED C18ORF34 WILD-TYPE 
                 5                  8 
  C18ORF34 MUTATED C18ORF34 WILD-TYPE 
                 4                  6 
$`C18ORF34 MUTATED`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A181 TCGA-EE-A182 TCGA-ER-A19F 
       30.87        10.03         1.12         1.35        11.11 

$`C18ORF34 WILD-TYPE`
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 
        6.64        11.57         1.08         9.47         2.43        23.90 
TCGA-FW-A3I3 TCGA-GN-A266 
        0.20        10.09 

  C18ORF34 MUTATED C18ORF34 WILD-TYPE 
              1.12               0.20 
  C18ORF34 MUTATED C18ORF34 WILD-TYPE 
             30.87              23.90 
  C18ORF34 MUTATED C18ORF34 WILD-TYPE 
            10.030              8.055 
[1] "1.1 - 30.9 (10.0)" "0.2 - 23.9 (8.1)" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "C18ORF34 MUTATED"   "C18ORF34 MUTATED" "C18ORF34 WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"C18ORF34 WILD-TYPE"   "C18ORF34 MUTATED"   "C18ORF34 MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"C18ORF34 WILD-TYPE" "C18ORF34 WILD-TYPE" "C18ORF34 WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-ER-A19F         TCGA-FW-A3I3 
"C18ORF34 WILD-TYPE"   "C18ORF34 MUTATED" "C18ORF34 WILD-TYPE" 
        TCGA-GN-A266 
"C18ORF34 WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "C18ORF34 MUTATED"   "C18ORF34 MUTATED" "C18ORF34 WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"C18ORF34 WILD-TYPE"   "C18ORF34 MUTATED"   "C18ORF34 MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"C18ORF34 WILD-TYPE" "C18ORF34 WILD-TYPE" "C18ORF34 WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-ER-A19F         TCGA-FW-A3I3 
"C18ORF34 WILD-TYPE"   "C18ORF34 MUTATED" "C18ORF34 WILD-TYPE" 
        TCGA-GN-A266 
"C18ORF34 WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "C18ORF34 MUTATED"   "C18ORF34 MUTATED" "C18ORF34 WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"C18ORF34 WILD-TYPE"   "C18ORF34 MUTATED"   "C18ORF34 MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"C18ORF34 WILD-TYPE" "C18ORF34 WILD-TYPE" "C18ORF34 WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-ER-A19F         TCGA-FW-A3I3 
"C18ORF34 WILD-TYPE"   "C18ORF34 MUTATED" "C18ORF34 WILD-TYPE" 
        TCGA-GN-A266 
"C18ORF34 WILD-TYPE" 
[1] "hr=" "1.1"
D30V2, continuous
                    vv
clus                 DISTANT METASTASIS
  C18ORF34 MUTATED                    4
  C18ORF34 WILD-TYPE                  3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  C18ORF34 MUTATED                                                                                          1
  C18ORF34 WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  C18ORF34 MUTATED                     5
  C18ORF34 WILD-TYPE                   8
D30V3, multiclass
                                                                                          clus
vv                                                                                         C18ORF34 MUTATED
  DISTANT METASTASIS                                                                                      4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         C18ORF34 WILD-TYPE
  DISTANT METASTASIS                                                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                       8
D30V4, binary
                    cls
clus                  0  1
  C18ORF34 MUTATED    4  6
  C18ORF34 WILD-TYPE  4 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C18ORF34 MUTATED      4    6
  C18ORF34 WILD-TYPE    4   11
        clus
vv       C18ORF34 MUTATED C18ORF34 WILD-TYPE
  FEMALE                4                  4
  MALE                  6                 11
                    vv
clus                 N0 N1B N2C N3
  C18ORF34 MUTATED    7   1   1  1
  C18ORF34 WILD-TYPE  9   2   1  1
D30V5, multiclass
     clus
vv    C18ORF34 MUTATED C18ORF34 WILD-TYPE
  N0                 7                  9
  N1B                1                  2
  N2C                1                  1
  N3                 1                  1
D30V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  C18ORF34 MUTATED          1        0        3         2          1          2
  C18ORF34 WILD-TYPE        2        1        3         1          2          2
                    vv
clus                 STAGE IV
  C18ORF34 MUTATED          0
  C18ORF34 WILD-TYPE        1
D30V7, multiclass

Clustering(31) Variable = FRG2B MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2             0 1
  FRG2B MUTATED   0 2
  FRG2B WILD-TYPE 3 8
  FRG2B MUTATED FRG2B WILD-TYPE 
              2              11 
  FRG2B MUTATED FRG2B WILD-TYPE 
              2               8 
$`FRG2B MUTATED`
TCGA-EE-A181 TCGA-EE-A182 
        1.12         1.35 

$`FRG2B WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29N 
       30.87        10.03         6.64        11.57         1.08         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        2.43        23.90        11.11         0.20        10.09 

  FRG2B MUTATED FRG2B WILD-TYPE 
           1.12            0.20 
  FRG2B MUTATED FRG2B WILD-TYPE 
           1.35           30.87 
  FRG2B MUTATED FRG2B WILD-TYPE 
          1.235          10.030 
[1] "1.1 - 1.4 (1.2)"   "0.2 - 30.9 (10.0)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "FRG2B MUTATED"   "FRG2B MUTATED" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" 
     TCGA-GN-A266 
"FRG2B WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "FRG2B MUTATED"   "FRG2B MUTATED" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" 
     TCGA-GN-A266 
"FRG2B WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "FRG2B MUTATED"   "FRG2B MUTATED" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" 
     TCGA-GN-A266 
"FRG2B WILD-TYPE" 
[1] "Remove cluster labels:" "FRG2B MUTATED"         
clus
  FRG2B MUTATED FRG2B WILD-TYPE 
              2              11 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" 
     TCGA-EE-A29L      TCGA-EE-A29N      TCGA-EE-A29V      TCGA-EE-A2A2 
"FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" 
     TCGA-ER-A19F      TCGA-FW-A3I3      TCGA-GN-A266 
"FRG2B WILD-TYPE" "FRG2B WILD-TYPE" "FRG2B WILD-TYPE" 
D31V2, continuous
                 vv
clus              DISTANT METASTASIS
  FRG2B MUTATED                    1
  FRG2B WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  FRG2B MUTATED                                                                                          2
  FRG2B WILD-TYPE                                                                                        3
                 vv
clus              REGIONAL LYMPH NODE
  FRG2B MUTATED                     2
  FRG2B WILD-TYPE                  11
D31V3, multiclass
                                                                                          clus
vv                                                                                         FRG2B MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  2
                                                                                          clus
vv                                                                                         FRG2B WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                   11
D31V4, binary
                 cls
clus               0  1
  FRG2B MUTATED    4  1
  FRG2B WILD-TYPE  4 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FRG2B MUTATED      4    1
  FRG2B WILD-TYPE    4   16
        clus
vv       FRG2B MUTATED FRG2B WILD-TYPE
  FEMALE             4               4
  MALE               1              16
                 vv
clus              N0 N1B N2C N3
  FRG2B MUTATED    4   1   0  0
  FRG2B WILD-TYPE 12   2   2  2
D31V5, multiclass
     clus
vv    FRG2B MUTATED FRG2B WILD-TYPE
  N0              4              12
  N1B             1               2
  N2C             0               2
  N3              0               2
D31V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  FRG2B MUTATED          1        0        3         0          0          1
  FRG2B WILD-TYPE        2        1        3         3          3          3
                 vv
clus              STAGE IV
  FRG2B MUTATED          0
  FRG2B WILD-TYPE        1
D31V7, multiclass

Clustering(32) Variable = LPPR1 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2             0 1
  LPPR1 MUTATED   0 3
  LPPR1 WILD-TYPE 3 7
  LPPR1 MUTATED LPPR1 WILD-TYPE 
              3              10 
  LPPR1 MUTATED LPPR1 WILD-TYPE 
              3               7 
$`LPPR1 MUTATED`
TCGA-EE-A29L TCGA-EE-A29N TCGA-GN-A266 
        1.08         9.47        10.09 

$`LPPR1 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       30.87        10.03         6.64        11.57         1.12         1.35 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 
        2.43        23.90        11.11         0.20 

  LPPR1 MUTATED LPPR1 WILD-TYPE 
           1.08            0.20 
  LPPR1 MUTATED LPPR1 WILD-TYPE 
          10.09           30.87 
  LPPR1 MUTATED LPPR1 WILD-TYPE 
          9.470           8.335 
[1] "1.1 - 10.1 (9.5)" "0.2 - 30.9 (8.3)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE"   "LPPR1 MUTATED"   "LPPR1 MUTATED" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" 
     TCGA-GN-A266 
  "LPPR1 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE"   "LPPR1 MUTATED"   "LPPR1 MUTATED" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" 
     TCGA-GN-A266 
  "LPPR1 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE"   "LPPR1 MUTATED"   "LPPR1 MUTATED" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" 
     TCGA-GN-A266 
  "LPPR1 MUTATED" 
[1] "hr=" "2.1"
D32V2, continuous
                 vv
clus              DISTANT METASTASIS
  LPPR1 MUTATED                    0
  LPPR1 WILD-TYPE                  7
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  LPPR1 MUTATED                                                                                          1
  LPPR1 WILD-TYPE                                                                                        4
                 vv
clus              REGIONAL LYMPH NODE
  LPPR1 MUTATED                     3
  LPPR1 WILD-TYPE                  10
D32V3, multiclass
                                                                                          clus
vv                                                                                         LPPR1 MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         LPPR1 WILD-TYPE
  DISTANT METASTASIS                                                                                     7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                   10
D32V4, binary
                 cls
clus               0  1
  LPPR1 MUTATED    0  4
  LPPR1 WILD-TYPE  8 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPPR1 MUTATED      0    4
  LPPR1 WILD-TYPE    8   13
        clus
vv       LPPR1 MUTATED LPPR1 WILD-TYPE
  FEMALE             0               8
  MALE               4              13
                 vv
clus              N0 N1B N2C N3
  LPPR1 MUTATED    2   0   0  1
  LPPR1 WILD-TYPE 14   3   2  1
D32V5, multiclass
     clus
vv    LPPR1 MUTATED LPPR1 WILD-TYPE
  N0              2              14
  N1B             0               3
  N2C             0               2
  N3              1               1
D32V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  LPPR1 MUTATED          0        0        1         0          0          1
  LPPR1 WILD-TYPE        3        1        5         3          3          3
                 vv
clus              STAGE IV
  LPPR1 MUTATED          0
  LPPR1 WILD-TYPE        1
D32V7, multiclass
[1] "Remove cluster labels:" "LPPR1 MUTATED"         
clus
  LPPR1 MUTATED LPPR1 WILD-TYPE 
              2              19 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29V      TCGA-EE-A2A2 
"LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" 
     TCGA-EE-A2GC      TCGA-EE-A2GO      TCGA-EE-A2GR      TCGA-EE-A2MI 
"LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" 
     TCGA-EE-A2MJ      TCGA-EE-A2MT      TCGA-EE-A3AE      TCGA-FS-A1ZA 
"LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" 
     TCGA-FS-A1ZP      TCGA-FS-A1ZZ      TCGA-FW-A3I3 
"LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" "LPPR1 WILD-TYPE" 

Clustering(33) Variable = THEMIS MUTATION ANALYSIS
D33V1, survival
                  sevent
clus2              0 1
  THEMIS MUTATED   0 2
  THEMIS WILD-TYPE 3 8
  THEMIS MUTATED THEMIS WILD-TYPE 
               2               11 
  THEMIS MUTATED THEMIS WILD-TYPE 
               2                8 
$`THEMIS MUTATED`
TCGA-EE-A17X TCGA-EE-A29L 
       11.57         1.08 

$`THEMIS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29N 
       30.87        10.03         6.64         1.12         1.35         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        2.43        23.90        11.11         0.20        10.09 

  THEMIS MUTATED THEMIS WILD-TYPE 
            1.08             0.20 
  THEMIS MUTATED THEMIS WILD-TYPE 
           11.57            30.87 
  THEMIS MUTATED THEMIS WILD-TYPE 
           6.325            9.470 
[1] "1.1 - 11.6 (6.3)" "0.2 - 30.9 (9.5)"
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE"   "THEMIS MUTATED" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE"   "THEMIS MUTATED" "THEMIS WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-GN-A266 
"THEMIS WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE"   "THEMIS MUTATED" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE"   "THEMIS MUTATED" "THEMIS WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-GN-A266 
"THEMIS WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE"   "THEMIS MUTATED" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE"   "THEMIS MUTATED" "THEMIS WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-GN-A266 
"THEMIS WILD-TYPE" 
[1] "Remove cluster labels:" "THEMIS MUTATED"        
clus
  THEMIS MUTATED THEMIS WILD-TYPE 
               2               11 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A181 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-EE-A182       TCGA-EE-A29N       TCGA-EE-A29V       TCGA-EE-A2A2 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
      TCGA-ER-A19F       TCGA-FW-A3I3       TCGA-GN-A266 
"THEMIS WILD-TYPE" "THEMIS WILD-TYPE" "THEMIS WILD-TYPE" 
D33V2, continuous
                  vv
clus               DISTANT METASTASIS
  THEMIS MUTATED                    1
  THEMIS WILD-TYPE                  6
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  THEMIS MUTATED                                                                                          1
  THEMIS WILD-TYPE                                                                                        4
                  vv
clus               REGIONAL LYMPH NODE
  THEMIS MUTATED                     5
  THEMIS WILD-TYPE                   8
D33V3, multiclass
                                                                                          clus
vv                                                                                         THEMIS MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   5
                                                                                          clus
vv                                                                                         THEMIS WILD-TYPE
  DISTANT METASTASIS                                                                                      6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                     8
D33V4, binary
                  cls
clus                0  1
  THEMIS MUTATED    3  4
  THEMIS WILD-TYPE  5 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THEMIS MUTATED      3    4
  THEMIS WILD-TYPE    5   13
        clus
vv       THEMIS MUTATED THEMIS WILD-TYPE
  FEMALE              3                5
  MALE                4               13
                  vv
clus               N0 N1B N2C N3
  THEMIS MUTATED    5   0   1  1
  THEMIS WILD-TYPE 11   3   1  1
D33V5, multiclass
     clus
vv    THEMIS MUTATED THEMIS WILD-TYPE
  N0               5               11
  N1B              0                3
  N2C              1                1
  N3               1                1
D33V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  THEMIS MUTATED          2        0        2         1          1          1
  THEMIS WILD-TYPE        1        1        4         2          2          3
                  vv
clus               STAGE IV
  THEMIS MUTATED          0
  THEMIS WILD-TYPE        1
D33V7, multiclass

Clustering(34) Variable = SNAP91 MUTATION ANALYSIS
D34V1, survival
                  sevent
clus2              0 1
  SNAP91 MUTATED   0 3
  SNAP91 WILD-TYPE 3 7
  SNAP91 MUTATED SNAP91 WILD-TYPE 
               3               10 
  SNAP91 MUTATED SNAP91 WILD-TYPE 
               3                7 
$`SNAP91 MUTATED`
TCGA-EE-A17X TCGA-EE-A182 TCGA-GN-A266 
       11.57         1.35        10.09 

$`SNAP91 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29N 
       30.87        10.03         6.64         1.12         1.08         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 
        2.43        23.90        11.11         0.20 

  SNAP91 MUTATED SNAP91 WILD-TYPE 
            1.35             0.20 
  SNAP91 MUTATED SNAP91 WILD-TYPE 
           11.57            30.87 
  SNAP91 MUTATED SNAP91 WILD-TYPE 
          10.090            8.055 
[1] "1.4 - 11.6 (10.1)" "0.2 - 30.9 (8.1)" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE"   "SNAP91 MUTATED" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"SNAP91 WILD-TYPE"   "SNAP91 MUTATED" "SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE" 
      TCGA-GN-A266 
  "SNAP91 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE"   "SNAP91 MUTATED" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"SNAP91 WILD-TYPE"   "SNAP91 MUTATED" "SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE" 
      TCGA-GN-A266 
  "SNAP91 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE"   "SNAP91 MUTATED" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"SNAP91 WILD-TYPE"   "SNAP91 MUTATED" "SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE" "SNAP91 WILD-TYPE" 
      TCGA-GN-A266 
  "SNAP91 MUTATED" 
[1] "hr=" "1.1"
D34V2, continuous
                  vv
clus               DISTANT METASTASIS
  SNAP91 MUTATED                    1
  SNAP91 WILD-TYPE                  6
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  SNAP91 MUTATED                                                                                          1
  SNAP91 WILD-TYPE                                                                                        4
                  vv
clus               REGIONAL LYMPH NODE
  SNAP91 MUTATED                     5
  SNAP91 WILD-TYPE                   8
D34V3, multiclass
                                                                                          clus
vv                                                                                         SNAP91 MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   5
                                                                                          clus
vv                                                                                         SNAP91 WILD-TYPE
  DISTANT METASTASIS                                                                                      6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                     8
D34V4, binary
                  cls
clus                0  1
  SNAP91 MUTATED    1  6
  SNAP91 WILD-TYPE  7 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAP91 MUTATED      1    6
  SNAP91 WILD-TYPE    7   11
        clus
vv       SNAP91 MUTATED SNAP91 WILD-TYPE
  FEMALE              1                7
  MALE                6               11
                  vv
clus               N0 N1B N2C N3
  SNAP91 MUTATED    5   1   0  0
  SNAP91 WILD-TYPE 11   2   2  2
D34V5, multiclass
     clus
vv    SNAP91 MUTATED SNAP91 WILD-TYPE
  N0               5               11
  N1B              1                2
  N2C              0                2
  N3               0                2
D34V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  SNAP91 MUTATED          1        1        1         2          0          1
  SNAP91 WILD-TYPE        2        0        5         1          3          3
                  vv
clus               STAGE IV
  SNAP91 MUTATED          0
  SNAP91 WILD-TYPE        1
D34V7, multiclass

Clustering(35) Variable = SLC27A6 MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2               0 1
  SLC27A6 MUTATED   0 3
  SLC27A6 WILD-TYPE 3 7
  SLC27A6 MUTATED SLC27A6 WILD-TYPE 
                3                10 
  SLC27A6 MUTATED SLC27A6 WILD-TYPE 
                3                 7 
$`SLC27A6 MUTATED`
TCGA-EE-A181 TCGA-EE-A182 TCGA-ER-A19F 
        1.12         1.35        11.11 

$`SLC27A6 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29N 
       30.87        10.03         6.64        11.57         1.08         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-FW-A3I3 TCGA-GN-A266 
        2.43        23.90         0.20        10.09 

  SLC27A6 MUTATED SLC27A6 WILD-TYPE 
             1.12              0.20 
  SLC27A6 MUTATED SLC27A6 WILD-TYPE 
            11.11             30.87 
  SLC27A6 MUTATED SLC27A6 WILD-TYPE 
             1.35              9.75 
[1] "1.1 - 11.1 (1.4)" "0.2 - 30.9 (9.8)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"SLC27A6 WILD-TYPE" "SLC27A6 WILD-TYPE" "SLC27A6 WILD-TYPE" "SLC27A6 WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "SLC27A6 MUTATED"   "SLC27A6 MUTATED" "SLC27A6 WILD-TYPE" "SLC27A6 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"SLC27A6 WILD-TYPE" "SLC27A6 WILD-TYPE"   "SLC27A6 MUTATED" "SLC27A6 WILD-TYPE" 
       TCGA-GN-A266 
"SLC27A6 WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"SLC27A6 WILD-TYPE" "SLC27A6 WILD-TYPE" "SLC27A6 WILD-TYPE" "SLC27A6 WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "SLC27A6 MUTATED"   "SLC27A6 MUTATED" "SLC27A6 WILD-TYPE" "SLC27A6 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"SLC27A6 WILD-TYPE" "SLC27A6 WILD-TYPE"   "SLC27A6 MUTATED" "SLC27A6 WILD-TYPE" 
       TCGA-GN-A266 
"SLC27A6 WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"SLC27A6 WILD-TYPE" "SLC27A6 WILD-TYPE" "SLC27A6 WILD-TYPE" "SLC27A6 WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "SLC27A6 MUTATED"   "SLC27A6 MUTATED" "SLC27A6 WILD-TYPE" "SLC27A6 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"SLC27A6 WILD-TYPE" "SLC27A6 WILD-TYPE"   "SLC27A6 MUTATED" "SLC27A6 WILD-TYPE" 
       TCGA-GN-A266 
"SLC27A6 WILD-TYPE" 
[1] "hr=" "2.2"
D35V2, continuous
                   vv
clus                DISTANT METASTASIS
  SLC27A6 MUTATED                    1
  SLC27A6 WILD-TYPE                  6
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  SLC27A6 MUTATED                                                                                          2
  SLC27A6 WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  SLC27A6 MUTATED                     5
  SLC27A6 WILD-TYPE                   8
D35V3, multiclass
                                                                                          clus
vv                                                                                         SLC27A6 MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         SLC27A6 WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                      8
D35V4, binary
                   cls
clus                 0  1
  SLC27A6 MUTATED    3  5
  SLC27A6 WILD-TYPE  5 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A6 MUTATED      3    5
  SLC27A6 WILD-TYPE    5   12
        clus
vv       SLC27A6 MUTATED SLC27A6 WILD-TYPE
  FEMALE               3                 5
  MALE                 5                12
                   vv
clus                N0 N1B N2C N3
  SLC27A6 MUTATED    7   1   0  0
  SLC27A6 WILD-TYPE  9   2   2  2
D35V5, multiclass
     clus
vv    SLC27A6 MUTATED SLC27A6 WILD-TYPE
  N0                7                 9
  N1B               1                 2
  N2C               0                 2
  N3                0                 2
D35V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  SLC27A6 MUTATED          0        0        5         1          0          1
  SLC27A6 WILD-TYPE        3        1        1         2          3          3
                   vv
clus                STAGE IV
  SLC27A6 MUTATED          0
  SLC27A6 WILD-TYPE        1
D35V7, multiclass

Clustering(36) Variable = CXORF22 MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2               0 1
  CXORF22 MUTATED   0 3
  CXORF22 WILD-TYPE 3 7
  CXORF22 MUTATED CXORF22 WILD-TYPE 
                3                10 
  CXORF22 MUTATED CXORF22 WILD-TYPE 
                3                 7 
$`CXORF22 MUTATED`
TCGA-EE-A182 TCGA-EE-A29L TCGA-GN-A266 
        1.35         1.08        10.09 

$`CXORF22 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29N 
       30.87        10.03         6.64        11.57         1.12         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 
        2.43        23.90        11.11         0.20 

  CXORF22 MUTATED CXORF22 WILD-TYPE 
             1.08              0.20 
  CXORF22 MUTATED CXORF22 WILD-TYPE 
            10.09             30.87 
  CXORF22 MUTATED CXORF22 WILD-TYPE 
             1.35              9.75 
[1] "1.1 - 10.1 (1.4)" "0.2 - 30.9 (9.8)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"CXORF22 WILD-TYPE"   "CXORF22 MUTATED"   "CXORF22 MUTATED" "CXORF22 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" 
       TCGA-GN-A266 
  "CXORF22 MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"CXORF22 WILD-TYPE"   "CXORF22 MUTATED"   "CXORF22 MUTATED" "CXORF22 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" 
       TCGA-GN-A266 
  "CXORF22 MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"CXORF22 WILD-TYPE"   "CXORF22 MUTATED"   "CXORF22 MUTATED" "CXORF22 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" "CXORF22 WILD-TYPE" 
       TCGA-GN-A266 
  "CXORF22 MUTATED" 
[1] "hr=" "2.9"
D36V2, continuous
                   vv
clus                DISTANT METASTASIS
  CXORF22 MUTATED                    3
  CXORF22 WILD-TYPE                  4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CXORF22 MUTATED                                                                                          2
  CXORF22 WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  CXORF22 MUTATED                     3
  CXORF22 WILD-TYPE                  10
D36V3, multiclass
                                                                                          clus
vv                                                                                         CXORF22 MUTATED
  DISTANT METASTASIS                                                                                     3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         CXORF22 WILD-TYPE
  DISTANT METASTASIS                                                                                       4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     10
D36V4, binary
                   cls
clus                 0  1
  CXORF22 MUTATED    4  4
  CXORF22 WILD-TYPE  4 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CXORF22 MUTATED      4    4
  CXORF22 WILD-TYPE    4   13
        clus
vv       CXORF22 MUTATED CXORF22 WILD-TYPE
  FEMALE               4                 4
  MALE                 4                13
                   vv
clus                N0 N1B N2C N3
  CXORF22 MUTATED    3   1   1  1
  CXORF22 WILD-TYPE 13   2   1  1
D36V5, multiclass
     clus
vv    CXORF22 MUTATED CXORF22 WILD-TYPE
  N0                3                13
  N1B               1                 2
  N2C               1                 1
  N3                1                 1
D36V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  CXORF22 MUTATED          0        0        2         1          1          2
  CXORF22 WILD-TYPE        3        1        4         2          2          2
                   vv
clus                STAGE IV
  CXORF22 MUTATED          0
  CXORF22 WILD-TYPE        1
D36V7, multiclass

Clustering(37) Variable = NOBOX MUTATION ANALYSIS
D37V1, survival
                 sevent
clus2             0 1
  NOBOX MUTATED   0 2
  NOBOX WILD-TYPE 3 8
  NOBOX MUTATED NOBOX WILD-TYPE 
              2              11 
  NOBOX MUTATED NOBOX WILD-TYPE 
              2               8 
$`NOBOX MUTATED`
TCGA-DA-A1IC TCGA-EE-A181 
        6.64         1.12 

$`NOBOX WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
       30.87        10.03        11.57         1.35         1.08         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        2.43        23.90        11.11         0.20        10.09 

  NOBOX MUTATED NOBOX WILD-TYPE 
           1.12            0.20 
  NOBOX MUTATED NOBOX WILD-TYPE 
           6.64           30.87 
  NOBOX MUTATED NOBOX WILD-TYPE 
           3.88           10.03 
[1] "1.1 - 6.6 (3.9)"   "0.2 - 30.9 (10.0)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE"   "NOBOX MUTATED" "NOBOX WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "NOBOX MUTATED" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-GN-A266 
"NOBOX WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE"   "NOBOX MUTATED" "NOBOX WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "NOBOX MUTATED" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-GN-A266 
"NOBOX WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE"   "NOBOX MUTATED" "NOBOX WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "NOBOX MUTATED" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-GN-A266 
"NOBOX WILD-TYPE" 
[1] "Remove cluster labels:" "NOBOX MUTATED"         
clus
  NOBOX MUTATED NOBOX WILD-TYPE 
              2              11 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-EE-A17X      TCGA-EE-A182 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-EE-A29L      TCGA-EE-A29N      TCGA-EE-A29V      TCGA-EE-A2A2 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
     TCGA-ER-A19F      TCGA-FW-A3I3      TCGA-GN-A266 
"NOBOX WILD-TYPE" "NOBOX WILD-TYPE" "NOBOX WILD-TYPE" 
D37V2, continuous
                 vv
clus              DISTANT METASTASIS
  NOBOX MUTATED                    1
  NOBOX WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  NOBOX MUTATED                                                                                          2
  NOBOX WILD-TYPE                                                                                        3
                 vv
clus              REGIONAL LYMPH NODE
  NOBOX MUTATED                     5
  NOBOX WILD-TYPE                   8
D37V3, multiclass
                                                                                          clus
vv                                                                                         NOBOX MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  5
                                                                                          clus
vv                                                                                         NOBOX WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    8
D37V4, binary
                 cls
clus               0  1
  NOBOX MUTATED    3  5
  NOBOX WILD-TYPE  5 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOBOX MUTATED      3    5
  NOBOX WILD-TYPE    5   12
        clus
vv       NOBOX MUTATED NOBOX WILD-TYPE
  FEMALE             3               5
  MALE               5              12
                 vv
clus              N0 N1B N2C N3
  NOBOX MUTATED    6   0   1  0
  NOBOX WILD-TYPE 10   3   1  2
D37V5, multiclass
     clus
vv    NOBOX MUTATED NOBOX WILD-TYPE
  N0              6              10
  N1B             0               3
  N2C             1               1
  N3              0               2
D37V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  NOBOX MUTATED          1        0        3         2          1          0
  NOBOX WILD-TYPE        2        1        3         1          2          4
                 vv
clus              STAGE IV
  NOBOX MUTATED          0
  NOBOX WILD-TYPE        1
D37V7, multiclass

Clustering(38) Variable = MUC7 MUTATION ANALYSIS
D38V1, survival
                sevent
clus2            0 1
  MUC7 MUTATED   0 2
  MUC7 WILD-TYPE 3 8
  MUC7 MUTATED MUC7 WILD-TYPE 
             2             11 
  MUC7 MUTATED MUC7 WILD-TYPE 
             2              8 
$`MUC7 MUTATED`
TCGA-DA-A1IC TCGA-EE-A181 
        6.64         1.12 

$`MUC7 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
       30.87        10.03        11.57         1.35         1.08         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        2.43        23.90        11.11         0.20        10.09 

  MUC7 MUTATED MUC7 WILD-TYPE 
          1.12           0.20 
  MUC7 MUTATED MUC7 WILD-TYPE 
          6.64          30.87 
  MUC7 MUTATED MUC7 WILD-TYPE 
          3.88          10.03 
[1] "1.1 - 6.6 (3.9)"   "0.2 - 30.9 (10.0)"
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"MUC7 WILD-TYPE" "MUC7 WILD-TYPE"   "MUC7 MUTATED" "MUC7 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "MUC7 MUTATED" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"MUC7 WILD-TYPE" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" 
    TCGA-GN-A266 
"MUC7 WILD-TYPE" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"MUC7 WILD-TYPE" "MUC7 WILD-TYPE"   "MUC7 MUTATED" "MUC7 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "MUC7 MUTATED" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"MUC7 WILD-TYPE" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" 
    TCGA-GN-A266 
"MUC7 WILD-TYPE" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"MUC7 WILD-TYPE" "MUC7 WILD-TYPE"   "MUC7 MUTATED" "MUC7 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "MUC7 MUTATED" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"MUC7 WILD-TYPE" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" 
    TCGA-GN-A266 
"MUC7 WILD-TYPE" 
[1] "Remove cluster labels:" "MUC7 MUTATED"          
clus
  MUC7 MUTATED MUC7 WILD-TYPE 
             2             11 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-EE-A17X     TCGA-EE-A182 
"MUC7 WILD-TYPE" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" 
    TCGA-EE-A29L     TCGA-EE-A29N     TCGA-EE-A29V     TCGA-EE-A2A2 
"MUC7 WILD-TYPE" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" 
    TCGA-ER-A19F     TCGA-FW-A3I3     TCGA-GN-A266 
"MUC7 WILD-TYPE" "MUC7 WILD-TYPE" "MUC7 WILD-TYPE" 
D38V2, continuous
                vv
clus             DISTANT METASTASIS
  MUC7 MUTATED                    0
  MUC7 WILD-TYPE                  7
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  MUC7 MUTATED                                                                                          2
  MUC7 WILD-TYPE                                                                                        3
                vv
clus             REGIONAL LYMPH NODE
  MUC7 MUTATED                     3
  MUC7 WILD-TYPE                  10
D38V3, multiclass
                                                                                          clus
vv                                                                                         MUC7 MUTATED
  DISTANT METASTASIS                                                                                  0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            2
  REGIONAL LYMPH NODE                                                                                 3
                                                                                          clus
vv                                                                                         MUC7 WILD-TYPE
  DISTANT METASTASIS                                                                                    7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              3
  REGIONAL LYMPH NODE                                                                                  10
D38V4, binary
                cls
clus              0  1
  MUC7 MUTATED    2  3
  MUC7 WILD-TYPE  6 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      2    3
  MUC7 WILD-TYPE    6   14
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  FEMALE            2              6
  MALE              3             14
                vv
clus             N0 N1B N2C N3
  MUC7 MUTATED    4   0   1  0
  MUC7 WILD-TYPE 12   3   1  2
D38V5, multiclass
     clus
vv    MUC7 MUTATED MUC7 WILD-TYPE
  N0             4             12
  N1B            0              3
  N2C            1              1
  N3             0              2
D38V6, continuous
                vv
clus             STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  MUC7 MUTATED          0        0        3         1          1          0
  MUC7 WILD-TYPE        3        1        3         2          2          4
                vv
clus             STAGE IV
  MUC7 MUTATED          0
  MUC7 WILD-TYPE        1
D38V7, multiclass

Clustering(39) Variable = GIMAP7 MUTATION ANALYSIS
D39V1, survival
                  sevent
clus2              0 1
  GIMAP7 MUTATED   1 3
  GIMAP7 WILD-TYPE 2 7
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
               4                9 
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
               3                7 
$`GIMAP7 MUTATED`
TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A2A2 TCGA-GN-A266 
        1.35         1.08        23.90        10.09 

$`GIMAP7 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29N 
       30.87        10.03         6.64        11.57         1.12         9.47 
TCGA-EE-A29V TCGA-ER-A19F TCGA-FW-A3I3 
        2.43        11.11         0.20 

  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
            1.08             0.20 
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
           23.90            30.87 
  GIMAP7 MUTATED GIMAP7 WILD-TYPE 
            5.72             9.47 
[1] "1.1 - 23.9 (5.7)" "0.2 - 30.9 (9.5)"
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"GIMAP7 WILD-TYPE"   "GIMAP7 MUTATED"   "GIMAP7 MUTATED" "GIMAP7 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"GIMAP7 WILD-TYPE"   "GIMAP7 MUTATED" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-GN-A266 
  "GIMAP7 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"GIMAP7 WILD-TYPE"   "GIMAP7 MUTATED"   "GIMAP7 MUTATED" "GIMAP7 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"GIMAP7 WILD-TYPE"   "GIMAP7 MUTATED" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-GN-A266 
  "GIMAP7 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"GIMAP7 WILD-TYPE"   "GIMAP7 MUTATED"   "GIMAP7 MUTATED" "GIMAP7 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"GIMAP7 WILD-TYPE"   "GIMAP7 MUTATED" "GIMAP7 WILD-TYPE" "GIMAP7 WILD-TYPE" 
      TCGA-GN-A266 
  "GIMAP7 MUTATED" 
[1] "hr=" "1"  
D39V2, continuous
                  vv
clus               DISTANT METASTASIS
  GIMAP7 MUTATED                    1
  GIMAP7 WILD-TYPE                  6
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  GIMAP7 MUTATED                                                                                          1
  GIMAP7 WILD-TYPE                                                                                        4
                  vv
clus               REGIONAL LYMPH NODE
  GIMAP7 MUTATED                     3
  GIMAP7 WILD-TYPE                  10
D39V3, multiclass
                                                                                          clus
vv                                                                                         GIMAP7 MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   3
                                                                                          clus
vv                                                                                         GIMAP7 WILD-TYPE
  DISTANT METASTASIS                                                                                      6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                    10
D39V4, binary
                  cls
clus                0  1
  GIMAP7 MUTATED    1  4
  GIMAP7 WILD-TYPE  7 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP7 MUTATED      1    4
  GIMAP7 WILD-TYPE    7   13
        clus
vv       GIMAP7 MUTATED GIMAP7 WILD-TYPE
  FEMALE              1                7
  MALE                4               13
                  vv
clus               N0 N1B N2C N3
  GIMAP7 MUTATED    1   2   0  1
  GIMAP7 WILD-TYPE 15   1   2  1
D39V5, multiclass
     clus
vv    GIMAP7 MUTATED GIMAP7 WILD-TYPE
  N0               1               15
  N1B              2                1
  N2C              0                2
  N3               1                1
D39V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  GIMAP7 MUTATED          0        1        0         0          1          2
  GIMAP7 WILD-TYPE        3        0        6         3          2          2
                  vv
clus               STAGE IV
  GIMAP7 MUTATED          0
  GIMAP7 WILD-TYPE        1
D39V7, multiclass

Clustering(40) Variable = SYT17 MUTATION ANALYSIS
D40V1, survival
                 sevent
clus2             0 1
  SYT17 MUTATED   1 2
  SYT17 WILD-TYPE 2 8
  SYT17 MUTATED SYT17 WILD-TYPE 
              3              10 
  SYT17 MUTATED SYT17 WILD-TYPE 
              2               8 
$`SYT17 MUTATED`
TCGA-DA-A1IC TCGA-EE-A29L TCGA-EE-A2A2 
        6.64         1.08        23.90 

$`SYT17 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29N 
       30.87        10.03        11.57         1.12         1.35         9.47 
TCGA-EE-A29V TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        2.43        11.11         0.20        10.09 

  SYT17 MUTATED SYT17 WILD-TYPE 
           1.08            0.20 
  SYT17 MUTATED SYT17 WILD-TYPE 
          23.90           30.87 
  SYT17 MUTATED SYT17 WILD-TYPE 
           6.64            9.75 
[1] "1.1 - 23.9 (6.6)" "0.2 - 30.9 (9.8)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"SYT17 WILD-TYPE" "SYT17 WILD-TYPE"   "SYT17 MUTATED" "SYT17 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"SYT17 WILD-TYPE" "SYT17 WILD-TYPE"   "SYT17 MUTATED" "SYT17 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"SYT17 WILD-TYPE"   "SYT17 MUTATED" "SYT17 WILD-TYPE" "SYT17 WILD-TYPE" 
     TCGA-GN-A266 
"SYT17 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"SYT17 WILD-TYPE" "SYT17 WILD-TYPE"   "SYT17 MUTATED" "SYT17 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"SYT17 WILD-TYPE" "SYT17 WILD-TYPE"   "SYT17 MUTATED" "SYT17 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"SYT17 WILD-TYPE"   "SYT17 MUTATED" "SYT17 WILD-TYPE" "SYT17 WILD-TYPE" 
     TCGA-GN-A266 
"SYT17 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"SYT17 WILD-TYPE" "SYT17 WILD-TYPE"   "SYT17 MUTATED" "SYT17 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"SYT17 WILD-TYPE" "SYT17 WILD-TYPE"   "SYT17 MUTATED" "SYT17 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"SYT17 WILD-TYPE"   "SYT17 MUTATED" "SYT17 WILD-TYPE" "SYT17 WILD-TYPE" 
     TCGA-GN-A266 
"SYT17 WILD-TYPE" 
[1] "hr=" "1.1"
D40V2, continuous
                 vv
clus              DISTANT METASTASIS
  SYT17 MUTATED                    0
  SYT17 WILD-TYPE                  7
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  SYT17 MUTATED                                                                                          2
  SYT17 WILD-TYPE                                                                                        3
                 vv
clus              REGIONAL LYMPH NODE
  SYT17 MUTATED                     3
  SYT17 WILD-TYPE                  10
D40V3, multiclass
                                                                                          clus
vv                                                                                         SYT17 MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         SYT17 WILD-TYPE
  DISTANT METASTASIS                                                                                     7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                   10
D40V4, binary
                 cls
clus               0  1
  SYT17 MUTATED    1  4
  SYT17 WILD-TYPE  7 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT17 MUTATED      1    4
  SYT17 WILD-TYPE    7   13
        clus
vv       SYT17 MUTATED SYT17 WILD-TYPE
  FEMALE             1               7
  MALE               4              13
                 vv
clus              N0 N1B N2C N3
  SYT17 MUTATED    2   1   1  1
  SYT17 WILD-TYPE 14   2   1  1
D40V5, multiclass
     clus
vv    SYT17 MUTATED SYT17 WILD-TYPE
  N0              2              14
  N1B             1               2
  N2C             1               1
  N3              1               1
D40V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  SYT17 MUTATED          1        0        1         0          2          1
  SYT17 WILD-TYPE        2        1        5         3          1          3
                 vv
clus              STAGE IV
  SYT17 MUTATED          0
  SYT17 WILD-TYPE        1
D40V7, multiclass

Clustering(41) Variable = ASB15 MUTATION ANALYSIS
D41V1, survival
                 sevent
clus2             0 1
  ASB15 MUTATED   0 6
  ASB15 WILD-TYPE 3 4
  ASB15 MUTATED ASB15 WILD-TYPE 
              6               7 
  ASB15 MUTATED ASB15 WILD-TYPE 
              6               4 
$`ASB15 MUTATED`
TCGA-DA-A1I0 TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29V TCGA-ER-A19F TCGA-GN-A266 
       10.03         1.12         1.08         2.43        11.11        10.09 

$`ASB15 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29N TCGA-EE-A2A2 
       30.87         6.64        11.57         1.35         9.47        23.90 
TCGA-FW-A3I3 
        0.20 

  ASB15 MUTATED ASB15 WILD-TYPE 
           1.08            0.20 
  ASB15 MUTATED ASB15 WILD-TYPE 
          11.11           30.87 
  ASB15 MUTATED ASB15 WILD-TYPE 
           6.23            9.47 
[1] "1.1 - 11.1 (6.2)" "0.2 - 30.9 (9.5)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"ASB15 WILD-TYPE"   "ASB15 MUTATED" "ASB15 WILD-TYPE" "ASB15 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "ASB15 MUTATED" "ASB15 WILD-TYPE"   "ASB15 MUTATED" "ASB15 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "ASB15 MUTATED" "ASB15 WILD-TYPE"   "ASB15 MUTATED" "ASB15 WILD-TYPE" 
     TCGA-GN-A266 
  "ASB15 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"ASB15 WILD-TYPE"   "ASB15 MUTATED" "ASB15 WILD-TYPE" "ASB15 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "ASB15 MUTATED" "ASB15 WILD-TYPE"   "ASB15 MUTATED" "ASB15 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "ASB15 MUTATED" "ASB15 WILD-TYPE"   "ASB15 MUTATED" "ASB15 WILD-TYPE" 
     TCGA-GN-A266 
  "ASB15 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"ASB15 WILD-TYPE"   "ASB15 MUTATED" "ASB15 WILD-TYPE" "ASB15 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "ASB15 MUTATED" "ASB15 WILD-TYPE"   "ASB15 MUTATED" "ASB15 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "ASB15 MUTATED" "ASB15 WILD-TYPE"   "ASB15 MUTATED" "ASB15 WILD-TYPE" 
     TCGA-GN-A266 
  "ASB15 MUTATED" 
[1] "hr=" "2.9"
D41V2, continuous
                 vv
clus              DISTANT METASTASIS
  ASB15 MUTATED                    2
  ASB15 WILD-TYPE                  5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ASB15 MUTATED                                                                                          2
  ASB15 WILD-TYPE                                                                                        3
                 vv
clus              REGIONAL LYMPH NODE
  ASB15 MUTATED                     4
  ASB15 WILD-TYPE                   9
D41V3, multiclass
                                                                                          clus
vv                                                                                         ASB15 MUTATED
  DISTANT METASTASIS                                                                                   2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  4
                                                                                          clus
vv                                                                                         ASB15 WILD-TYPE
  DISTANT METASTASIS                                                                                     5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    9
D41V4, binary
                 cls
clus               0  1
  ASB15 MUTATED    2  6
  ASB15 WILD-TYPE  6 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB15 MUTATED      2    6
  ASB15 WILD-TYPE    6   11
        clus
vv       ASB15 MUTATED ASB15 WILD-TYPE
  FEMALE             2               6
  MALE               6              11
                 vv
clus              N0 N1B N2C N3
  ASB15 MUTATED    3   1   0  2
  ASB15 WILD-TYPE 13   2   2  0
D41V5, multiclass
     clus
vv    ASB15 MUTATED ASB15 WILD-TYPE
  N0              3              13
  N1B             1               2
  N2C             0               2
  N3              2               0
D41V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  ASB15 MUTATED          0        0        1         1          0          3
  ASB15 WILD-TYPE        3        1        5         2          3          1
                 vv
clus              STAGE IV
  ASB15 MUTATED          0
  ASB15 WILD-TYPE        1
D41V7, multiclass

Clustering(42) Variable = OR4A15 MUTATION ANALYSIS
D42V1, survival
                  sevent
clus2              0 1
  OR4A15 MUTATED   1 2
  OR4A15 WILD-TYPE 2 8
  OR4A15 MUTATED OR4A15 WILD-TYPE 
               3               10 
  OR4A15 MUTATED OR4A15 WILD-TYPE 
               2                8 
$`OR4A15 MUTATED`
TCGA-EE-A182 TCGA-EE-A29V TCGA-EE-A2A2 
        1.35         2.43        23.90 

$`OR4A15 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29L 
       30.87        10.03         6.64        11.57         1.12         1.08 
TCGA-EE-A29N TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        9.47        11.11         0.20        10.09 

  OR4A15 MUTATED OR4A15 WILD-TYPE 
            1.35             0.20 
  OR4A15 MUTATED OR4A15 WILD-TYPE 
           23.90            30.87 
  OR4A15 MUTATED OR4A15 WILD-TYPE 
            2.43             9.75 
[1] "1.4 - 23.9 (2.4)" "0.2 - 30.9 (9.8)"
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"OR4A15 WILD-TYPE" "OR4A15 WILD-TYPE" "OR4A15 WILD-TYPE" "OR4A15 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"OR4A15 WILD-TYPE"   "OR4A15 MUTATED" "OR4A15 WILD-TYPE" "OR4A15 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
  "OR4A15 MUTATED"   "OR4A15 MUTATED" "OR4A15 WILD-TYPE" "OR4A15 WILD-TYPE" 
      TCGA-GN-A266 
"OR4A15 WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"OR4A15 WILD-TYPE" "OR4A15 WILD-TYPE" "OR4A15 WILD-TYPE" "OR4A15 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"OR4A15 WILD-TYPE"   "OR4A15 MUTATED" "OR4A15 WILD-TYPE" "OR4A15 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
  "OR4A15 MUTATED"   "OR4A15 MUTATED" "OR4A15 WILD-TYPE" "OR4A15 WILD-TYPE" 
      TCGA-GN-A266 
"OR4A15 WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"OR4A15 WILD-TYPE" "OR4A15 WILD-TYPE" "OR4A15 WILD-TYPE" "OR4A15 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"OR4A15 WILD-TYPE"   "OR4A15 MUTATED" "OR4A15 WILD-TYPE" "OR4A15 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
  "OR4A15 MUTATED"   "OR4A15 MUTATED" "OR4A15 WILD-TYPE" "OR4A15 WILD-TYPE" 
      TCGA-GN-A266 
"OR4A15 WILD-TYPE" 
[1] "hr=" "1.2"
D42V2, continuous
                  vv
clus               DISTANT METASTASIS
  OR4A15 MUTATED                    3
  OR4A15 WILD-TYPE                  4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  OR4A15 MUTATED                                                                                          0
  OR4A15 WILD-TYPE                                                                                        5
                  vv
clus               REGIONAL LYMPH NODE
  OR4A15 MUTATED                     3
  OR4A15 WILD-TYPE                  10
D42V3, multiclass
                                                                                          clus
vv                                                                                         OR4A15 MUTATED
  DISTANT METASTASIS                                                                                    3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              0
  REGIONAL LYMPH NODE                                                                                   3
                                                                                          clus
vv                                                                                         OR4A15 WILD-TYPE
  DISTANT METASTASIS                                                                                      4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    10
D42V4, binary
                  cls
clus                0  1
  OR4A15 MUTATED    2  4
  OR4A15 WILD-TYPE  6 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4A15 MUTATED      2    4
  OR4A15 WILD-TYPE    6   13
        clus
vv       OR4A15 MUTATED OR4A15 WILD-TYPE
  FEMALE              2                6
  MALE                4               13
                  vv
clus               N0 N1B N2C N3
  OR4A15 MUTATED    2   3   0  0
  OR4A15 WILD-TYPE 14   0   2  2
D42V5, multiclass
     clus
vv    OR4A15 MUTATED OR4A15 WILD-TYPE
  N0               2               14
  N1B              3                0
  N2C              0                2
  N3               0                2
D42V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  OR4A15 MUTATED          0        0        1         1          1          2
  OR4A15 WILD-TYPE        3        1        5         2          2          2
                  vv
clus               STAGE IV
  OR4A15 MUTATED          0
  OR4A15 WILD-TYPE        1
D42V7, multiclass

Clustering(43) Variable = PROL1 MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2             0 1
  PROL1 MUTATED   1 3
  PROL1 WILD-TYPE 2 7
  PROL1 MUTATED PROL1 WILD-TYPE 
              4               9 
  PROL1 MUTATED PROL1 WILD-TYPE 
              3               7 
$`PROL1 MUTATED`
TCGA-DA-A1I0 TCGA-EE-A182 TCGA-EE-A29N TCGA-EE-A2A2 
       10.03         1.35         9.47        23.90 

$`PROL1 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29V 
       30.87         6.64        11.57         1.12         1.08         2.43 
TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
       11.11         0.20        10.09 

  PROL1 MUTATED PROL1 WILD-TYPE 
           1.35            0.20 
  PROL1 MUTATED PROL1 WILD-TYPE 
          23.90           30.87 
  PROL1 MUTATED PROL1 WILD-TYPE 
           9.75            6.64 
[1] "1.4 - 23.9 (9.8)" "0.2 - 30.9 (6.6)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"PROL1 WILD-TYPE"   "PROL1 MUTATED" "PROL1 WILD-TYPE" "PROL1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"PROL1 WILD-TYPE"   "PROL1 MUTATED" "PROL1 WILD-TYPE"   "PROL1 MUTATED" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"PROL1 WILD-TYPE"   "PROL1 MUTATED" "PROL1 WILD-TYPE" "PROL1 WILD-TYPE" 
     TCGA-GN-A266 
"PROL1 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"PROL1 WILD-TYPE"   "PROL1 MUTATED" "PROL1 WILD-TYPE" "PROL1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"PROL1 WILD-TYPE"   "PROL1 MUTATED" "PROL1 WILD-TYPE"   "PROL1 MUTATED" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"PROL1 WILD-TYPE"   "PROL1 MUTATED" "PROL1 WILD-TYPE" "PROL1 WILD-TYPE" 
     TCGA-GN-A266 
"PROL1 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"PROL1 WILD-TYPE"   "PROL1 MUTATED" "PROL1 WILD-TYPE" "PROL1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"PROL1 WILD-TYPE"   "PROL1 MUTATED" "PROL1 WILD-TYPE"   "PROL1 MUTATED" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"PROL1 WILD-TYPE"   "PROL1 MUTATED" "PROL1 WILD-TYPE" "PROL1 WILD-TYPE" 
     TCGA-GN-A266 
"PROL1 WILD-TYPE" 
[1] "hr=" "1.2"
D43V2, continuous
                 vv
clus              DISTANT METASTASIS
  PROL1 MUTATED                    1
  PROL1 WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  PROL1 MUTATED                                                                                          2
  PROL1 WILD-TYPE                                                                                        3
                 vv
clus              REGIONAL LYMPH NODE
  PROL1 MUTATED                     4
  PROL1 WILD-TYPE                   9
D43V3, multiclass
                                                                                          clus
vv                                                                                         PROL1 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  4
                                                                                          clus
vv                                                                                         PROL1 WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    9
D43V4, binary
                 cls
clus               0  1
  PROL1 MUTATED    1  6
  PROL1 WILD-TYPE  7 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROL1 MUTATED      1    6
  PROL1 WILD-TYPE    7   11
        clus
vv       PROL1 MUTATED PROL1 WILD-TYPE
  FEMALE             1               7
  MALE               6              11
                 vv
clus              N0 N1B N2C N3
  PROL1 MUTATED    4   2   0  1
  PROL1 WILD-TYPE 12   1   2  1
D43V5, multiclass
     clus
vv    PROL1 MUTATED PROL1 WILD-TYPE
  N0              4              12
  N1B             2               1
  N2C             0               2
  N3              1               1
D43V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  PROL1 MUTATED          0        0        2         1          1          2
  PROL1 WILD-TYPE        3        1        4         2          2          2
                 vv
clus              STAGE IV
  PROL1 MUTATED          0
  PROL1 WILD-TYPE        1
D43V7, multiclass

Clustering(44) Variable = DSG3 MUTATION ANALYSIS
D44V1, survival
                sevent
clus2            0 1
  DSG3 MUTATED   0 6
  DSG3 WILD-TYPE 3 4
  DSG3 MUTATED DSG3 WILD-TYPE 
             6              7 
  DSG3 MUTATED DSG3 WILD-TYPE 
             6              4 
$`DSG3 MUTATED`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L TCGA-GN-A266 
       10.03         6.64         1.12         1.35         1.08        10.09 

$`DSG3 WILD-TYPE`
TCGA-D3-A2JF TCGA-EE-A17X TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F 
       30.87        11.57         9.47         2.43        23.90        11.11 
TCGA-FW-A3I3 
        0.20 

  DSG3 MUTATED DSG3 WILD-TYPE 
          1.08           0.20 
  DSG3 MUTATED DSG3 WILD-TYPE 
         10.09          30.87 
  DSG3 MUTATED DSG3 WILD-TYPE 
         3.995         11.110 
[1] "1.1 - 10.1 (4.0)"  "0.2 - 30.9 (11.1)"
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"DSG3 WILD-TYPE"   "DSG3 MUTATED"   "DSG3 MUTATED" "DSG3 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "DSG3 MUTATED"   "DSG3 MUTATED"   "DSG3 MUTATED" "DSG3 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"DSG3 WILD-TYPE" "DSG3 WILD-TYPE" "DSG3 WILD-TYPE" "DSG3 WILD-TYPE" 
    TCGA-GN-A266 
  "DSG3 MUTATED" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"DSG3 WILD-TYPE"   "DSG3 MUTATED"   "DSG3 MUTATED" "DSG3 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "DSG3 MUTATED"   "DSG3 MUTATED"   "DSG3 MUTATED" "DSG3 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"DSG3 WILD-TYPE" "DSG3 WILD-TYPE" "DSG3 WILD-TYPE" "DSG3 WILD-TYPE" 
    TCGA-GN-A266 
  "DSG3 MUTATED" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
"DSG3 WILD-TYPE"   "DSG3 MUTATED"   "DSG3 MUTATED" "DSG3 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "DSG3 MUTATED"   "DSG3 MUTATED"   "DSG3 MUTATED" "DSG3 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"DSG3 WILD-TYPE" "DSG3 WILD-TYPE" "DSG3 WILD-TYPE" "DSG3 WILD-TYPE" 
    TCGA-GN-A266 
  "DSG3 MUTATED" 
[1] "hr=" "5.7"
D44V2, continuous
                vv
clus             DISTANT METASTASIS
  DSG3 MUTATED                    3
  DSG3 WILD-TYPE                  4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DSG3 MUTATED                                                                                          5
  DSG3 WILD-TYPE                                                                                        0
                vv
clus             REGIONAL LYMPH NODE
  DSG3 MUTATED                     5
  DSG3 WILD-TYPE                   8
D44V3, multiclass
                                                                                          clus
vv                                                                                         DSG3 MUTATED
  DISTANT METASTASIS                                                                                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            5
  REGIONAL LYMPH NODE                                                                                 5
                                                                                          clus
vv                                                                                         DSG3 WILD-TYPE
  DISTANT METASTASIS                                                                                    4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              0
  REGIONAL LYMPH NODE                                                                                   8
D44V4, binary
                cls
clus             0 1
  DSG3 MUTATED   5 8
  DSG3 WILD-TYPE 3 9
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED      5    8
  DSG3 WILD-TYPE    3    9
        clus
vv       DSG3 MUTATED DSG3 WILD-TYPE
  FEMALE            5              3
  MALE              8              9
                vv
clus             N0 N1B N2C N3
  DSG3 MUTATED    7   1   1  2
  DSG3 WILD-TYPE  9   2   1  0
D44V5, multiclass
     clus
vv    DSG3 MUTATED DSG3 WILD-TYPE
  N0             7              9
  N1B            1              2
  N2C            1              1
  N3             2              0
D44V6, continuous
                vv
clus             STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  DSG3 MUTATED          0        0        4         3          1          3
  DSG3 WILD-TYPE        3        1        2         0          2          1
                vv
clus             STAGE IV
  DSG3 MUTATED          0
  DSG3 WILD-TYPE        1
D44V7, multiclass

Clustering(45) Variable = OPRK1 MUTATION ANALYSIS
D45V1, survival
                 sevent
clus2             0 1
  OPRK1 MUTATED   1 2
  OPRK1 WILD-TYPE 2 8
  OPRK1 MUTATED OPRK1 WILD-TYPE 
              3              10 
  OPRK1 MUTATED OPRK1 WILD-TYPE 
              2               8 
$`OPRK1 MUTATED`
TCGA-D3-A2JF TCGA-EE-A181 TCGA-EE-A29L 
       30.87         1.12         1.08 

$`OPRK1 WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29N TCGA-EE-A29V 
       10.03         6.64        11.57         1.35         9.47         2.43 
TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
       23.90        11.11         0.20        10.09 

  OPRK1 MUTATED OPRK1 WILD-TYPE 
           1.08            0.20 
  OPRK1 MUTATED OPRK1 WILD-TYPE 
          30.87           23.90 
  OPRK1 MUTATED OPRK1 WILD-TYPE 
           1.12            9.75 
[1] "1.1 - 30.9 (1.1)" "0.2 - 23.9 (9.8)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "OPRK1 MUTATED" "OPRK1 WILD-TYPE" "OPRK1 WILD-TYPE" "OPRK1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "OPRK1 MUTATED" "OPRK1 WILD-TYPE"   "OPRK1 MUTATED" "OPRK1 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"OPRK1 WILD-TYPE" "OPRK1 WILD-TYPE" "OPRK1 WILD-TYPE" "OPRK1 WILD-TYPE" 
     TCGA-GN-A266 
"OPRK1 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "OPRK1 MUTATED" "OPRK1 WILD-TYPE" "OPRK1 WILD-TYPE" "OPRK1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "OPRK1 MUTATED" "OPRK1 WILD-TYPE"   "OPRK1 MUTATED" "OPRK1 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"OPRK1 WILD-TYPE" "OPRK1 WILD-TYPE" "OPRK1 WILD-TYPE" "OPRK1 WILD-TYPE" 
     TCGA-GN-A266 
"OPRK1 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "OPRK1 MUTATED" "OPRK1 WILD-TYPE" "OPRK1 WILD-TYPE" "OPRK1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "OPRK1 MUTATED" "OPRK1 WILD-TYPE"   "OPRK1 MUTATED" "OPRK1 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"OPRK1 WILD-TYPE" "OPRK1 WILD-TYPE" "OPRK1 WILD-TYPE" "OPRK1 WILD-TYPE" 
     TCGA-GN-A266 
"OPRK1 WILD-TYPE" 
[1] "hr=" "1.1"
D45V2, continuous
                 vv
clus              DISTANT METASTASIS
  OPRK1 MUTATED                    2
  OPRK1 WILD-TYPE                  5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  OPRK1 MUTATED                                                                                          1
  OPRK1 WILD-TYPE                                                                                        4
                 vv
clus              REGIONAL LYMPH NODE
  OPRK1 MUTATED                     6
  OPRK1 WILD-TYPE                   7
D45V3, multiclass
                                                                                          clus
vv                                                                                         OPRK1 MUTATED
  DISTANT METASTASIS                                                                                   2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  6
                                                                                          clus
vv                                                                                         OPRK1 WILD-TYPE
  DISTANT METASTASIS                                                                                     5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                    7
D45V4, binary
                 cls
clus               0  1
  OPRK1 MUTATED    3  6
  OPRK1 WILD-TYPE  5 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPRK1 MUTATED      3    6
  OPRK1 WILD-TYPE    5   11
        clus
vv       OPRK1 MUTATED OPRK1 WILD-TYPE
  FEMALE             3               5
  MALE               6              11
                 vv
clus              N0 N1B N2C N3
  OPRK1 MUTATED    7   0   1  1
  OPRK1 WILD-TYPE  9   3   1  1
D45V5, multiclass
     clus
vv    OPRK1 MUTATED OPRK1 WILD-TYPE
  N0              7               9
  N1B             0               3
  N2C             1               1
  N3              1               1
D45V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  OPRK1 MUTATED          1        0        4         2          1          1
  OPRK1 WILD-TYPE        2        1        2         1          2          3
                 vv
clus              STAGE IV
  OPRK1 MUTATED          0
  OPRK1 WILD-TYPE        1
D45V7, multiclass

Clustering(46) Variable = PCSK5 MUTATION ANALYSIS
D46V1, survival
                 sevent
clus2             0 1
  PCSK5 MUTATED   1 3
  PCSK5 WILD-TYPE 2 7
  PCSK5 MUTATED PCSK5 WILD-TYPE 
              4               9 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
              3               7 
$`PCSK5 MUTATED`
TCGA-DA-A1IC TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A2A2 
        6.64         1.35         1.08        23.90 

$`PCSK5 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A29V 
       30.87        10.03        11.57         1.12         9.47         2.43 
TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
       11.11         0.20        10.09 

  PCSK5 MUTATED PCSK5 WILD-TYPE 
           1.08            0.20 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
          23.90           30.87 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
          3.995          10.030 
[1] "1.1 - 23.9 (4.0)"  "0.2 - 30.9 (10.0)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"PCSK5 WILD-TYPE" "PCSK5 WILD-TYPE"   "PCSK5 MUTATED" "PCSK5 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"PCSK5 WILD-TYPE"   "PCSK5 MUTATED"   "PCSK5 MUTATED" "PCSK5 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"PCSK5 WILD-TYPE"   "PCSK5 MUTATED" "PCSK5 WILD-TYPE" "PCSK5 WILD-TYPE" 
     TCGA-GN-A266 
"PCSK5 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"PCSK5 WILD-TYPE" "PCSK5 WILD-TYPE"   "PCSK5 MUTATED" "PCSK5 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"PCSK5 WILD-TYPE"   "PCSK5 MUTATED"   "PCSK5 MUTATED" "PCSK5 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"PCSK5 WILD-TYPE"   "PCSK5 MUTATED" "PCSK5 WILD-TYPE" "PCSK5 WILD-TYPE" 
     TCGA-GN-A266 
"PCSK5 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"PCSK5 WILD-TYPE" "PCSK5 WILD-TYPE"   "PCSK5 MUTATED" "PCSK5 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"PCSK5 WILD-TYPE"   "PCSK5 MUTATED"   "PCSK5 MUTATED" "PCSK5 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"PCSK5 WILD-TYPE"   "PCSK5 MUTATED" "PCSK5 WILD-TYPE" "PCSK5 WILD-TYPE" 
     TCGA-GN-A266 
"PCSK5 WILD-TYPE" 
[1] "hr=" "1.3"
D46V2, continuous
                 vv
clus              DISTANT METASTASIS
  PCSK5 MUTATED                    2
  PCSK5 WILD-TYPE                  5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  PCSK5 MUTATED                                                                                          2
  PCSK5 WILD-TYPE                                                                                        3
                 vv
clus              REGIONAL LYMPH NODE
  PCSK5 MUTATED                     6
  PCSK5 WILD-TYPE                   7
D46V3, multiclass
                                                                                          clus
vv                                                                                         PCSK5 MUTATED
  DISTANT METASTASIS                                                                                   2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  6
                                                                                          clus
vv                                                                                         PCSK5 WILD-TYPE
  DISTANT METASTASIS                                                                                     5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    7
D46V4, binary
                 cls
clus               0  1
  PCSK5 MUTATED    3  7
  PCSK5 WILD-TYPE  5 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK5 MUTATED      3    7
  PCSK5 WILD-TYPE    5   10
        clus
vv       PCSK5 MUTATED PCSK5 WILD-TYPE
  FEMALE             3               5
  MALE               7              10
                 vv
clus              N0 N1B N2C N3
  PCSK5 MUTATED    5   2   2  1
  PCSK5 WILD-TYPE 11   1   0  1
D46V5, multiclass
     clus
vv    PCSK5 MUTATED PCSK5 WILD-TYPE
  N0              5              11
  N1B             2               1
  N2C             2               0
  N3              1               1
D46V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  PCSK5 MUTATED          1        0        3         1          3          2
  PCSK5 WILD-TYPE        2        1        3         2          0          2
                 vv
clus              STAGE IV
  PCSK5 MUTATED          0
  PCSK5 WILD-TYPE        1
D46V7, multiclass

Clustering(47) Variable = OR52A1 MUTATION ANALYSIS
D47V1, survival
                  sevent
clus2              0 1
  OR52A1 MUTATED   1 3
  OR52A1 WILD-TYPE 2 7
  OR52A1 MUTATED OR52A1 WILD-TYPE 
               4                9 
  OR52A1 MUTATED OR52A1 WILD-TYPE 
               3                7 
$`OR52A1 MUTATED`
TCGA-DA-A1I0 TCGA-EE-A29L TCGA-EE-A2A2 TCGA-GN-A266 
       10.03         1.08        23.90        10.09 

$`OR52A1 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29N 
       30.87         6.64        11.57         1.12         1.35         9.47 
TCGA-EE-A29V TCGA-ER-A19F TCGA-FW-A3I3 
        2.43        11.11         0.20 

  OR52A1 MUTATED OR52A1 WILD-TYPE 
            1.08             0.20 
  OR52A1 MUTATED OR52A1 WILD-TYPE 
           23.90            30.87 
  OR52A1 MUTATED OR52A1 WILD-TYPE 
           10.06             6.64 
[1] "1.1 - 23.9 (10.1)" "0.2 - 30.9 (6.6)" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"OR52A1 WILD-TYPE"   "OR52A1 MUTATED" "OR52A1 WILD-TYPE" "OR52A1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"OR52A1 WILD-TYPE" "OR52A1 WILD-TYPE"   "OR52A1 MUTATED" "OR52A1 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"OR52A1 WILD-TYPE"   "OR52A1 MUTATED" "OR52A1 WILD-TYPE" "OR52A1 WILD-TYPE" 
      TCGA-GN-A266 
  "OR52A1 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"OR52A1 WILD-TYPE"   "OR52A1 MUTATED" "OR52A1 WILD-TYPE" "OR52A1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"OR52A1 WILD-TYPE" "OR52A1 WILD-TYPE"   "OR52A1 MUTATED" "OR52A1 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"OR52A1 WILD-TYPE"   "OR52A1 MUTATED" "OR52A1 WILD-TYPE" "OR52A1 WILD-TYPE" 
      TCGA-GN-A266 
  "OR52A1 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"OR52A1 WILD-TYPE"   "OR52A1 MUTATED" "OR52A1 WILD-TYPE" "OR52A1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"OR52A1 WILD-TYPE" "OR52A1 WILD-TYPE"   "OR52A1 MUTATED" "OR52A1 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"OR52A1 WILD-TYPE"   "OR52A1 MUTATED" "OR52A1 WILD-TYPE" "OR52A1 WILD-TYPE" 
      TCGA-GN-A266 
  "OR52A1 MUTATED" 
[1] "hr=" "1.3"
D47V2, continuous
                  vv
clus               DISTANT METASTASIS
  OR52A1 MUTATED                    0
  OR52A1 WILD-TYPE                  7
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  OR52A1 MUTATED                                                                                          4
  OR52A1 WILD-TYPE                                                                                        1
                  vv
clus               REGIONAL LYMPH NODE
  OR52A1 MUTATED                     2
  OR52A1 WILD-TYPE                  11
D47V3, multiclass
                                                                                          clus
vv                                                                                         OR52A1 MUTATED
  DISTANT METASTASIS                                                                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              4
  REGIONAL LYMPH NODE                                                                                   2
                                                                                          clus
vv                                                                                         OR52A1 WILD-TYPE
  DISTANT METASTASIS                                                                                      7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                    11
D47V4, binary
                  cls
clus                0  1
  OR52A1 MUTATED    1  5
  OR52A1 WILD-TYPE  7 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52A1 MUTATED      1    5
  OR52A1 WILD-TYPE    7   12
        clus
vv       OR52A1 MUTATED OR52A1 WILD-TYPE
  FEMALE              1                7
  MALE                5               12
                  vv
clus               N0 N1B N2C N3
  OR52A1 MUTATED    2   1   0  2
  OR52A1 WILD-TYPE 14   2   2  0
D47V5, multiclass
     clus
vv    OR52A1 MUTATED OR52A1 WILD-TYPE
  N0               2               14
  N1B              1                2
  N2C              0                2
  N3               2                0
D47V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  OR52A1 MUTATED          0        0        2         0          1          2
  OR52A1 WILD-TYPE        3        1        4         3          2          2
                  vv
clus               STAGE IV
  OR52A1 MUTATED          0
  OR52A1 WILD-TYPE        1
D47V7, multiclass

Clustering(48) Variable = ACSM2B MUTATION ANALYSIS
D48V1, survival
                  sevent
clus2              0 1
  ACSM2B MUTATED   1 3
  ACSM2B WILD-TYPE 2 7
  ACSM2B MUTATED ACSM2B WILD-TYPE 
               4                9 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
               3                7 
$`ACSM2B MUTATED`
TCGA-D3-A2JF TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29V 
       30.87         1.35         1.08         2.43 

$`ACSM2B WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A2A2 
       10.03         6.64        11.57         1.12         9.47        23.90 
TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
       11.11         0.20        10.09 

  ACSM2B MUTATED ACSM2B WILD-TYPE 
            1.08             0.20 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
           30.87            23.90 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
            1.89            10.03 
[1] "1.1 - 30.9 (1.9)"  "0.2 - 23.9 (10.0)"
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
  "ACSM2B MUTATED" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"ACSM2B WILD-TYPE"   "ACSM2B MUTATED"   "ACSM2B MUTATED" "ACSM2B WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
  "ACSM2B MUTATED" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-GN-A266 
"ACSM2B WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
  "ACSM2B MUTATED" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"ACSM2B WILD-TYPE"   "ACSM2B MUTATED"   "ACSM2B MUTATED" "ACSM2B WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
  "ACSM2B MUTATED" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-GN-A266 
"ACSM2B WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
  "ACSM2B MUTATED" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"ACSM2B WILD-TYPE"   "ACSM2B MUTATED"   "ACSM2B MUTATED" "ACSM2B WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
  "ACSM2B MUTATED" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-GN-A266 
"ACSM2B WILD-TYPE" 
[1] "hr=" "1.4"
D48V2, continuous
                  vv
clus               DISTANT METASTASIS
  ACSM2B MUTATED                    3
  ACSM2B WILD-TYPE                  4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ACSM2B MUTATED                                                                                          0
  ACSM2B WILD-TYPE                                                                                        5
                  vv
clus               REGIONAL LYMPH NODE
  ACSM2B MUTATED                     5
  ACSM2B WILD-TYPE                   8
D48V3, multiclass
                                                                                          clus
vv                                                                                         ACSM2B MUTATED
  DISTANT METASTASIS                                                                                    3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              0
  REGIONAL LYMPH NODE                                                                                   5
                                                                                          clus
vv                                                                                         ACSM2B WILD-TYPE
  DISTANT METASTASIS                                                                                      4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                     8
D48V4, binary
                  cls
clus                0  1
  ACSM2B MUTATED    1  7
  ACSM2B WILD-TYPE  7 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSM2B MUTATED      1    7
  ACSM2B WILD-TYPE    7   10
        clus
vv       ACSM2B MUTATED ACSM2B WILD-TYPE
  FEMALE              1                7
  MALE                7               10
                  vv
clus               N0 N1B N2C N3
  ACSM2B MUTATED    5   2   0  1
  ACSM2B WILD-TYPE 11   1   2  1
D48V5, multiclass
     clus
vv    ACSM2B MUTATED ACSM2B WILD-TYPE
  N0               5               11
  N1B              2                1
  N2C              0                2
  N3               1                1
D48V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  ACSM2B MUTATED          1        1        1         2          0          3
  ACSM2B WILD-TYPE        2        0        5         1          3          1
                  vv
clus               STAGE IV
  ACSM2B MUTATED          0
  ACSM2B WILD-TYPE        1
D48V7, multiclass

Clustering(49) Variable = NOL4 MUTATION ANALYSIS
D49V1, survival
                sevent
clus2            0 1
  NOL4 MUTATED   2 4
  NOL4 WILD-TYPE 1 6
  NOL4 MUTATED NOL4 WILD-TYPE 
             6              7 
  NOL4 MUTATED NOL4 WILD-TYPE 
             4              6 
$`NOL4 MUTATED`
TCGA-D3-A2JF TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A2A2 TCGA-GN-A266 
       30.87         1.12         1.08         2.43        23.90        10.09 

$`NOL4 WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29N TCGA-ER-A19F 
       10.03         6.64        11.57         1.35         9.47        11.11 
TCGA-FW-A3I3 
        0.20 

  NOL4 MUTATED NOL4 WILD-TYPE 
          1.08           0.20 
  NOL4 MUTATED NOL4 WILD-TYPE 
         30.87          11.57 
  NOL4 MUTATED NOL4 WILD-TYPE 
          6.26           9.47 
[1] "1.1 - 30.9 (6.3)" "0.2 - 11.6 (9.5)"
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
  "NOL4 MUTATED" "NOL4 WILD-TYPE" "NOL4 WILD-TYPE" "NOL4 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "NOL4 MUTATED" "NOL4 WILD-TYPE"   "NOL4 MUTATED" "NOL4 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
  "NOL4 MUTATED"   "NOL4 MUTATED" "NOL4 WILD-TYPE" "NOL4 WILD-TYPE" 
    TCGA-GN-A266 
  "NOL4 MUTATED" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
  "NOL4 MUTATED" "NOL4 WILD-TYPE" "NOL4 WILD-TYPE" "NOL4 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "NOL4 MUTATED" "NOL4 WILD-TYPE"   "NOL4 MUTATED" "NOL4 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
  "NOL4 MUTATED"   "NOL4 MUTATED" "NOL4 WILD-TYPE" "NOL4 WILD-TYPE" 
    TCGA-GN-A266 
  "NOL4 MUTATED" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
  "NOL4 MUTATED" "NOL4 WILD-TYPE" "NOL4 WILD-TYPE" "NOL4 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "NOL4 MUTATED" "NOL4 WILD-TYPE"   "NOL4 MUTATED" "NOL4 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
  "NOL4 MUTATED"   "NOL4 MUTATED" "NOL4 WILD-TYPE" "NOL4 WILD-TYPE" 
    TCGA-GN-A266 
  "NOL4 MUTATED" 
[1] "hr=" "1.4"
D49V2, continuous
                vv
clus             DISTANT METASTASIS
  NOL4 MUTATED                    3
  NOL4 WILD-TYPE                  4
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  NOL4 MUTATED                                                                                          1
  NOL4 WILD-TYPE                                                                                        4
                vv
clus             REGIONAL LYMPH NODE
  NOL4 MUTATED                     7
  NOL4 WILD-TYPE                   6
D49V3, multiclass
                                                                                          clus
vv                                                                                         NOL4 MUTATED
  DISTANT METASTASIS                                                                                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            1
  REGIONAL LYMPH NODE                                                                                 7
                                                                                          clus
vv                                                                                         NOL4 WILD-TYPE
  DISTANT METASTASIS                                                                                    4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              4
  REGIONAL LYMPH NODE                                                                                   6
D49V4, binary
                cls
clus             0 1
  NOL4 MUTATED   2 9
  NOL4 WILD-TYPE 6 8
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL4 MUTATED      2    9
  NOL4 WILD-TYPE    6    8
        clus
vv       NOL4 MUTATED NOL4 WILD-TYPE
  FEMALE            2              6
  MALE              9              8
                vv
clus             N0 N1B N2C N3
  NOL4 MUTATED    7   2   0  1
  NOL4 WILD-TYPE  9   1   2  1
D49V5, multiclass
     clus
vv    NOL4 MUTATED NOL4 WILD-TYPE
  N0             7              9
  N1B            2              1
  N2C            0              2
  N3             1              1
D49V6, continuous
                vv
clus             STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  NOL4 MUTATED          1        0        4         2          1          2
  NOL4 WILD-TYPE        2        1        2         1          2          2
                vv
clus             STAGE IV
  NOL4 MUTATED          0
  NOL4 WILD-TYPE        1
D49V7, multiclass

Clustering(50) Variable = PPFIA2 MUTATION ANALYSIS
D50V1, survival
                  sevent
clus2              0 1
  PPFIA2 MUTATED   1 4
  PPFIA2 WILD-TYPE 2 6
  PPFIA2 MUTATED PPFIA2 WILD-TYPE 
               5                8 
  PPFIA2 MUTATED PPFIA2 WILD-TYPE 
               4                6 
$`PPFIA2 MUTATED`
TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A2A2 TCGA-GN-A266 
        1.35         1.08         2.43        23.90        10.09 

$`PPFIA2 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29N 
       30.87        10.03         6.64        11.57         1.12         9.47 
TCGA-ER-A19F TCGA-FW-A3I3 
       11.11         0.20 

  PPFIA2 MUTATED PPFIA2 WILD-TYPE 
            1.08             0.20 
  PPFIA2 MUTATED PPFIA2 WILD-TYPE 
           23.90            30.87 
  PPFIA2 MUTATED PPFIA2 WILD-TYPE 
            2.43             9.75 
[1] "1.1 - 23.9 (2.4)" "0.2 - 30.9 (9.8)"
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"PPFIA2 WILD-TYPE" "PPFIA2 WILD-TYPE" "PPFIA2 WILD-TYPE" "PPFIA2 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"PPFIA2 WILD-TYPE"   "PPFIA2 MUTATED"   "PPFIA2 MUTATED" "PPFIA2 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
  "PPFIA2 MUTATED"   "PPFIA2 MUTATED" "PPFIA2 WILD-TYPE" "PPFIA2 WILD-TYPE" 
      TCGA-GN-A266 
  "PPFIA2 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"PPFIA2 WILD-TYPE" "PPFIA2 WILD-TYPE" "PPFIA2 WILD-TYPE" "PPFIA2 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"PPFIA2 WILD-TYPE"   "PPFIA2 MUTATED"   "PPFIA2 MUTATED" "PPFIA2 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
  "PPFIA2 MUTATED"   "PPFIA2 MUTATED" "PPFIA2 WILD-TYPE" "PPFIA2 WILD-TYPE" 
      TCGA-GN-A266 
  "PPFIA2 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"PPFIA2 WILD-TYPE" "PPFIA2 WILD-TYPE" "PPFIA2 WILD-TYPE" "PPFIA2 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"PPFIA2 WILD-TYPE"   "PPFIA2 MUTATED"   "PPFIA2 MUTATED" "PPFIA2 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
  "PPFIA2 MUTATED"   "PPFIA2 MUTATED" "PPFIA2 WILD-TYPE" "PPFIA2 WILD-TYPE" 
      TCGA-GN-A266 
  "PPFIA2 MUTATED" 
[1] "hr=" "1.3"
D50V2, continuous
                  vv
clus               DISTANT METASTASIS
  PPFIA2 MUTATED                    3
  PPFIA2 WILD-TYPE                  4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  PPFIA2 MUTATED                                                                                          1
  PPFIA2 WILD-TYPE                                                                                        4
                  vv
clus               REGIONAL LYMPH NODE
  PPFIA2 MUTATED                     5
  PPFIA2 WILD-TYPE                   8
D50V3, multiclass
                                                                                          clus
vv                                                                                         PPFIA2 MUTATED
  DISTANT METASTASIS                                                                                    3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   5
                                                                                          clus
vv                                                                                         PPFIA2 WILD-TYPE
  DISTANT METASTASIS                                                                                      4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                     8
D50V4, binary
                  cls
clus                0  1
  PPFIA2 MUTATED    2  7
  PPFIA2 WILD-TYPE  6 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPFIA2 MUTATED      2    7
  PPFIA2 WILD-TYPE    6   10
        clus
vv       PPFIA2 MUTATED PPFIA2 WILD-TYPE
  FEMALE              2                6
  MALE                7               10
                  vv
clus               N0 N1B N2C N3
  PPFIA2 MUTATED    4   3   0  1
  PPFIA2 WILD-TYPE 12   0   2  1
D50V5, multiclass
     clus
vv    PPFIA2 MUTATED PPFIA2 WILD-TYPE
  N0               4               12
  N1B              3                0
  N2C              0                2
  N3               1                1
D50V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  PPFIA2 MUTATED          0        0        1         3          1          3
  PPFIA2 WILD-TYPE        3        1        5         0          2          1
                  vv
clus               STAGE IV
  PPFIA2 MUTATED          0
  PPFIA2 WILD-TYPE        1
D50V7, multiclass

Clustering(51) Variable = IL1F8 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2             0 1
  IL1F8 MUTATED   0 3
  IL1F8 WILD-TYPE 3 7
  IL1F8 MUTATED IL1F8 WILD-TYPE 
              3              10 
  IL1F8 MUTATED IL1F8 WILD-TYPE 
              3               7 
$`IL1F8 MUTATED`
TCGA-DA-A1I0 TCGA-EE-A29V TCGA-GN-A266 
       10.03         2.43        10.09 

$`IL1F8 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L 
       30.87         6.64        11.57         1.12         1.35         1.08 
TCGA-EE-A29N TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 
        9.47        23.90        11.11         0.20 

  IL1F8 MUTATED IL1F8 WILD-TYPE 
           2.43            0.20 
  IL1F8 MUTATED IL1F8 WILD-TYPE 
          10.09           30.87 
  IL1F8 MUTATED IL1F8 WILD-TYPE 
         10.030           8.055 
[1] "2.4 - 10.1 (10.0)" "0.2 - 30.9 (8.1)" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"IL1F8 WILD-TYPE"   "IL1F8 MUTATED" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "IL1F8 MUTATED" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-GN-A266 
  "IL1F8 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"IL1F8 WILD-TYPE"   "IL1F8 MUTATED" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "IL1F8 MUTATED" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-GN-A266 
  "IL1F8 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"IL1F8 WILD-TYPE"   "IL1F8 MUTATED" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
  "IL1F8 MUTATED" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-GN-A266 
  "IL1F8 MUTATED" 
[1] "hr=" "1.6"
D51V2, continuous
                 vv
clus              DISTANT METASTASIS
  IL1F8 MUTATED                    1
  IL1F8 WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  IL1F8 MUTATED                                                                                          3
  IL1F8 WILD-TYPE                                                                                        2
                 vv
clus              REGIONAL LYMPH NODE
  IL1F8 MUTATED                     1
  IL1F8 WILD-TYPE                  12
D51V3, multiclass
                                                                                          clus
vv                                                                                         IL1F8 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             3
  REGIONAL LYMPH NODE                                                                                  1
                                                                                          clus
vv                                                                                         IL1F8 WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                   12
D51V4, binary
                 cls
clus               0  1
  IL1F8 MUTATED    1  4
  IL1F8 WILD-TYPE  7 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1F8 MUTATED      1    4
  IL1F8 WILD-TYPE    7   13
        clus
vv       IL1F8 MUTATED IL1F8 WILD-TYPE
  FEMALE             1               7
  MALE               4              13
                 vv
clus              N0 N1B N2C N3
  IL1F8 MUTATED    2   1   0  1
  IL1F8 WILD-TYPE 14   2   2  1
D51V5, multiclass
     clus
vv    IL1F8 MUTATED IL1F8 WILD-TYPE
  N0              2              14
  N1B             1               2
  N2C             0               2
  N3              1               1
D51V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  IL1F8 MUTATED          0        0        1         1          0          2
  IL1F8 WILD-TYPE        3        1        5         2          3          2
                 vv
clus              STAGE IV
  IL1F8 MUTATED          0
  IL1F8 WILD-TYPE        1
D51V7, multiclass

Clustering(52) Variable = UGT2A1 MUTATION ANALYSIS
D52V1, survival
                  sevent
clus2              0 1
  UGT2A1 MUTATED   1 2
  UGT2A1 WILD-TYPE 2 8
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
               3               10 
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
               2                8 
$`UGT2A1 MUTATED`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A29L 
       30.87        10.03         1.08 

$`UGT2A1 WILD-TYPE`
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29N TCGA-EE-A29V 
        6.64        11.57         1.12         1.35         9.47         2.43 
TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
       23.90        11.11         0.20        10.09 

  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
            1.08             0.20 
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
           30.87            23.90 
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
          10.030            8.055 
[1] "1.1 - 30.9 (10.0)" "0.2 - 23.9 (8.1)" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
  "UGT2A1 MUTATED"   "UGT2A1 MUTATED" "UGT2A1 WILD-TYPE" "UGT2A1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"UGT2A1 WILD-TYPE" "UGT2A1 WILD-TYPE"   "UGT2A1 MUTATED" "UGT2A1 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"UGT2A1 WILD-TYPE" "UGT2A1 WILD-TYPE" "UGT2A1 WILD-TYPE" "UGT2A1 WILD-TYPE" 
      TCGA-GN-A266 
"UGT2A1 WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
  "UGT2A1 MUTATED"   "UGT2A1 MUTATED" "UGT2A1 WILD-TYPE" "UGT2A1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"UGT2A1 WILD-TYPE" "UGT2A1 WILD-TYPE"   "UGT2A1 MUTATED" "UGT2A1 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"UGT2A1 WILD-TYPE" "UGT2A1 WILD-TYPE" "UGT2A1 WILD-TYPE" "UGT2A1 WILD-TYPE" 
      TCGA-GN-A266 
"UGT2A1 WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
  "UGT2A1 MUTATED"   "UGT2A1 MUTATED" "UGT2A1 WILD-TYPE" "UGT2A1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"UGT2A1 WILD-TYPE" "UGT2A1 WILD-TYPE"   "UGT2A1 MUTATED" "UGT2A1 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"UGT2A1 WILD-TYPE" "UGT2A1 WILD-TYPE" "UGT2A1 WILD-TYPE" "UGT2A1 WILD-TYPE" 
      TCGA-GN-A266 
"UGT2A1 WILD-TYPE" 
[1] "hr=" "1.3"
D52V2, continuous
                  vv
clus               DISTANT METASTASIS
  UGT2A1 MUTATED                    1
  UGT2A1 WILD-TYPE                  6
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  UGT2A1 MUTATED                                                                                          3
  UGT2A1 WILD-TYPE                                                                                        2
                  vv
clus               REGIONAL LYMPH NODE
  UGT2A1 MUTATED                     2
  UGT2A1 WILD-TYPE                  11
D52V3, multiclass
                                                                                          clus
vv                                                                                         UGT2A1 MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              3
  REGIONAL LYMPH NODE                                                                                   2
                                                                                          clus
vv                                                                                         UGT2A1 WILD-TYPE
  DISTANT METASTASIS                                                                                      6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                    11
D52V4, binary
                  cls
clus                0  1
  UGT2A1 MUTATED    1  5
  UGT2A1 WILD-TYPE  7 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A1 MUTATED      1    5
  UGT2A1 WILD-TYPE    7   12
        clus
vv       UGT2A1 MUTATED UGT2A1 WILD-TYPE
  FEMALE              1                7
  MALE                5               12
                  vv
clus               N0 N1B N2C N3
  UGT2A1 MUTATED    4   0   0  2
  UGT2A1 WILD-TYPE 12   3   2  0
D52V5, multiclass
     clus
vv    UGT2A1 MUTATED UGT2A1 WILD-TYPE
  N0               4               12
  N1B              0                3
  N2C              0                2
  N3               2                0
D52V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  UGT2A1 MUTATED          1        0        2         1          0          2
  UGT2A1 WILD-TYPE        2        1        4         2          3          2
                  vv
clus               STAGE IV
  UGT2A1 MUTATED          0
  UGT2A1 WILD-TYPE        1
D52V7, multiclass

Clustering(53) Variable = SYT13 MUTATION ANALYSIS
D53V1, survival
                 sevent
clus2             0 1
  SYT13 MUTATED   0 1
  SYT13 WILD-TYPE 3 9
  SYT13 MUTATED SYT13 WILD-TYPE 
              1              12 
  SYT13 MUTATED SYT13 WILD-TYPE 
              1               9 
$`SYT13 MUTATED`
TCGA-GN-A266 
       10.09 

$`SYT13 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       30.87        10.03         6.64        11.57         1.12         1.35 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 
        1.08         9.47         2.43        23.90        11.11         0.20 

  SYT13 MUTATED SYT13 WILD-TYPE 
          10.09            0.20 
  SYT13 MUTATED SYT13 WILD-TYPE 
          10.09           30.87 
  SYT13 MUTATED SYT13 WILD-TYPE 
         10.090           8.055 
[1] "10.1 - 10.1 (10.1)" "0.2 - 30.9 (8.1)"  
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-GN-A266 
  "SYT13 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-GN-A266 
  "SYT13 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-GN-A266 
  "SYT13 MUTATED" 
[1] "Remove cluster labels:" "SYT13 MUTATED"         
clus
  SYT13 MUTATED SYT13 WILD-TYPE 
              1              12 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
D53V2, continuous
                 vv
clus              DISTANT METASTASIS
  SYT13 MUTATED                    0
  SYT13 WILD-TYPE                  7
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  SYT13 MUTATED                                                                                          2
  SYT13 WILD-TYPE                                                                                        3
                 vv
clus              REGIONAL LYMPH NODE
  SYT13 MUTATED                     1
  SYT13 WILD-TYPE                  12
D53V3, multiclass
                                                                                          clus
vv                                                                                         SYT13 MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  1
                                                                                          clus
vv                                                                                         SYT13 WILD-TYPE
  DISTANT METASTASIS                                                                                     7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                   12
D53V4, binary
                 cls
clus               0  1
  SYT13 MUTATED    1  2
  SYT13 WILD-TYPE  7 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT13 MUTATED      1    2
  SYT13 WILD-TYPE    7   15
        clus
vv       SYT13 MUTATED SYT13 WILD-TYPE
  FEMALE             1               7
  MALE               2              15
                 vv
clus              N0 N1B N2C N3
  SYT13 MUTATED    2   0   0  0
  SYT13 WILD-TYPE 14   3   2  2
D53V5, multiclass
[1] "Remove cluster labels:" "SYT13 MUTATED"         
clus
  SYT13 MUTATED SYT13 WILD-TYPE 
              2              21 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-EE-A2GC      TCGA-EE-A2GR 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-EE-A2MI      TCGA-EE-A2MJ      TCGA-EE-A2MT      TCGA-EE-A3AE 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-ER-A19F      TCGA-FS-A1ZA      TCGA-FS-A1ZP      TCGA-FS-A1ZZ 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-FW-A3I3 
"SYT13 WILD-TYPE" 
D53V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  SYT13 MUTATED          0        0        2         0          0          0
  SYT13 WILD-TYPE        3        1        4         3          3          4
                 vv
clus              STAGE IV
  SYT13 MUTATED          0
  SYT13 WILD-TYPE        1
D53V7, multiclass
[1] "Remove cluster labels:" "SYT13 MUTATED"         
clus
  SYT13 MUTATED SYT13 WILD-TYPE 
              2              19 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29V 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2GC      TCGA-EE-A2GR      TCGA-EE-A2MI 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-EE-A2MJ      TCGA-EE-A2MT      TCGA-EE-A3AE      TCGA-FS-A1ZA 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 
     TCGA-FS-A1ZP      TCGA-FS-A1ZZ      TCGA-FW-A3I3 
"SYT13 WILD-TYPE" "SYT13 WILD-TYPE" "SYT13 WILD-TYPE" 

Clustering(54) Variable = ASAH2 MUTATION ANALYSIS
D54V1, survival
                 sevent
clus2             0 1
  ASAH2 MUTATED   0 2
  ASAH2 WILD-TYPE 3 8
  ASAH2 MUTATED ASAH2 WILD-TYPE 
              2              11 
  ASAH2 MUTATED ASAH2 WILD-TYPE 
              2               8 
$`ASAH2 MUTATED`
TCGA-DA-A1IC TCGA-EE-A29L 
        6.64         1.08 

$`ASAH2 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29N 
       30.87        10.03        11.57         1.12         1.35         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        2.43        23.90        11.11         0.20        10.09 

  ASAH2 MUTATED ASAH2 WILD-TYPE 
           1.08            0.20 
  ASAH2 MUTATED ASAH2 WILD-TYPE 
           6.64           30.87 
  ASAH2 MUTATED ASAH2 WILD-TYPE 
           3.86           10.03 
[1] "1.1 - 6.6 (3.9)"   "0.2 - 30.9 (10.0)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE"   "ASAH2 MUTATED" "ASAH2 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE"   "ASAH2 MUTATED" "ASAH2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" 
     TCGA-GN-A266 
"ASAH2 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE"   "ASAH2 MUTATED" "ASAH2 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE"   "ASAH2 MUTATED" "ASAH2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" 
     TCGA-GN-A266 
"ASAH2 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE"   "ASAH2 MUTATED" "ASAH2 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE"   "ASAH2 MUTATED" "ASAH2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" 
     TCGA-GN-A266 
"ASAH2 WILD-TYPE" 
[1] "Remove cluster labels:" "ASAH2 MUTATED"         
clus
  ASAH2 MUTATED ASAH2 WILD-TYPE 
              2              11 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-EE-A17X      TCGA-EE-A181 
"ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" 
     TCGA-EE-A182      TCGA-EE-A29N      TCGA-EE-A29V      TCGA-EE-A2A2 
"ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" 
     TCGA-ER-A19F      TCGA-FW-A3I3      TCGA-GN-A266 
"ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" "ASAH2 WILD-TYPE" 
D54V2, continuous
                 vv
clus              DISTANT METASTASIS
  ASAH2 MUTATED                    1
  ASAH2 WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ASAH2 MUTATED                                                                                          1
  ASAH2 WILD-TYPE                                                                                        4
                 vv
clus              REGIONAL LYMPH NODE
  ASAH2 MUTATED                     4
  ASAH2 WILD-TYPE                   9
D54V3, multiclass
                                                                                          clus
vv                                                                                         ASAH2 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  4
                                                                                          clus
vv                                                                                         ASAH2 WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                    9
D54V4, binary
                 cls
clus               0  1
  ASAH2 MUTATED    1  5
  ASAH2 WILD-TYPE  7 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASAH2 MUTATED      1    5
  ASAH2 WILD-TYPE    7   12
        clus
vv       ASAH2 MUTATED ASAH2 WILD-TYPE
  FEMALE             1               7
  MALE               5              12
                 vv
clus              N0 N1B N2C N3
  ASAH2 MUTATED    4   0   1  1
  ASAH2 WILD-TYPE 12   3   1  1
D54V5, multiclass
     clus
vv    ASAH2 MUTATED ASAH2 WILD-TYPE
  N0              4              12
  N1B             0               3
  N2C             1               1
  N3              1               1
D54V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  ASAH2 MUTATED          0        1        1         2          1          1
  ASAH2 WILD-TYPE        3        0        5         1          2          3
                 vv
clus              STAGE IV
  ASAH2 MUTATED          0
  ASAH2 WILD-TYPE        1
D54V7, multiclass

Clustering(55) Variable = ZNF679 MUTATION ANALYSIS
D55V1, survival
                  sevent
clus2              0 1
  ZNF679 MUTATED   0 2
  ZNF679 WILD-TYPE 3 8
  ZNF679 MUTATED ZNF679 WILD-TYPE 
               2               11 
  ZNF679 MUTATED ZNF679 WILD-TYPE 
               2                8 
$`ZNF679 MUTATED`
TCGA-EE-A182 TCGA-GN-A266 
        1.35        10.09 

$`ZNF679 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29L 
       30.87        10.03         6.64        11.57         1.12         1.08 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 
        9.47         2.43        23.90        11.11         0.20 

  ZNF679 MUTATED ZNF679 WILD-TYPE 
            1.35             0.20 
  ZNF679 MUTATED ZNF679 WILD-TYPE 
           10.09            30.87 
  ZNF679 MUTATED ZNF679 WILD-TYPE 
            5.72             9.47 
[1] "1.4 - 10.1 (5.7)" "0.2 - 30.9 (9.5)"
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"ZNF679 WILD-TYPE"   "ZNF679 MUTATED" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" 
      TCGA-GN-A266 
  "ZNF679 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"ZNF679 WILD-TYPE"   "ZNF679 MUTATED" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" 
      TCGA-GN-A266 
  "ZNF679 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"ZNF679 WILD-TYPE"   "ZNF679 MUTATED" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" 
      TCGA-GN-A266 
  "ZNF679 MUTATED" 
[1] "Remove cluster labels:" "ZNF679 MUTATED"        
clus
  ZNF679 MUTATED ZNF679 WILD-TYPE 
               2               11 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A29L       TCGA-EE-A29N       TCGA-EE-A29V 
"ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" "ZNF679 WILD-TYPE" 
D55V2, continuous
                  vv
clus               DISTANT METASTASIS
  ZNF679 MUTATED                    2
  ZNF679 WILD-TYPE                  5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ZNF679 MUTATED                                                                                          2
  ZNF679 WILD-TYPE                                                                                        3
                  vv
clus               REGIONAL LYMPH NODE
  ZNF679 MUTATED                     3
  ZNF679 WILD-TYPE                  10
D55V3, multiclass
                                                                                          clus
vv                                                                                         ZNF679 MUTATED
  DISTANT METASTASIS                                                                                    2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              2
  REGIONAL LYMPH NODE                                                                                   3
                                                                                          clus
vv                                                                                         ZNF679 WILD-TYPE
  DISTANT METASTASIS                                                                                      5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                    10
D55V4, binary
                  cls
clus                0  1
  ZNF679 MUTATED    2  5
  ZNF679 WILD-TYPE  6 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF679 MUTATED      2    5
  ZNF679 WILD-TYPE    6   12
        clus
vv       ZNF679 MUTATED ZNF679 WILD-TYPE
  FEMALE              2                6
  MALE                5               12
                  vv
clus               N0 N1B N2C N3
  ZNF679 MUTATED    5   1   0  0
  ZNF679 WILD-TYPE 11   2   2  2
D55V5, multiclass
     clus
vv    ZNF679 MUTATED ZNF679 WILD-TYPE
  N0               5               11
  N1B              1                2
  N2C              0                2
  N3               0                2
D55V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  ZNF679 MUTATED          0        1        2         2          0          1
  ZNF679 WILD-TYPE        3        0        4         1          3          3
                  vv
clus               STAGE IV
  ZNF679 MUTATED          0
  ZNF679 WILD-TYPE        1
D55V7, multiclass

Clustering(56) Variable = C10ORF54 MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                0 1
  C10ORF54 MUTATED   1 2
  C10ORF54 WILD-TYPE 2 8
  C10ORF54 MUTATED C10ORF54 WILD-TYPE 
                 3                 10 
  C10ORF54 MUTATED C10ORF54 WILD-TYPE 
                 2                  8 
$`C10ORF54 MUTATED`
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A2A2 
        6.64        11.57        23.90 

$`C10ORF54 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
       30.87        10.03         1.12         1.35         1.08         9.47 
TCGA-EE-A29V TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        2.43        11.11         0.20        10.09 

  C10ORF54 MUTATED C10ORF54 WILD-TYPE 
              6.64               0.20 
  C10ORF54 MUTATED C10ORF54 WILD-TYPE 
             23.90              30.87 
  C10ORF54 MUTATED C10ORF54 WILD-TYPE 
             11.57               5.95 
[1] "6.6 - 23.9 (11.6)" "0.2 - 30.9 (6.0)" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"C10ORF54 WILD-TYPE" "C10ORF54 WILD-TYPE"   "C10ORF54 MUTATED" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
  "C10ORF54 MUTATED" "C10ORF54 WILD-TYPE" "C10ORF54 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"C10ORF54 WILD-TYPE" "C10ORF54 WILD-TYPE" "C10ORF54 WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-ER-A19F         TCGA-FW-A3I3 
  "C10ORF54 MUTATED" "C10ORF54 WILD-TYPE" "C10ORF54 WILD-TYPE" 
        TCGA-GN-A266 
"C10ORF54 WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"C10ORF54 WILD-TYPE" "C10ORF54 WILD-TYPE"   "C10ORF54 MUTATED" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
  "C10ORF54 MUTATED" "C10ORF54 WILD-TYPE" "C10ORF54 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"C10ORF54 WILD-TYPE" "C10ORF54 WILD-TYPE" "C10ORF54 WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-ER-A19F         TCGA-FW-A3I3 
  "C10ORF54 MUTATED" "C10ORF54 WILD-TYPE" "C10ORF54 WILD-TYPE" 
        TCGA-GN-A266 
"C10ORF54 WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"C10ORF54 WILD-TYPE" "C10ORF54 WILD-TYPE"   "C10ORF54 MUTATED" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
  "C10ORF54 MUTATED" "C10ORF54 WILD-TYPE" "C10ORF54 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"C10ORF54 WILD-TYPE" "C10ORF54 WILD-TYPE" "C10ORF54 WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-ER-A19F         TCGA-FW-A3I3 
  "C10ORF54 MUTATED" "C10ORF54 WILD-TYPE" "C10ORF54 WILD-TYPE" 
        TCGA-GN-A266 
"C10ORF54 WILD-TYPE" 
[1] "hr=" "2.5"
D56V2, continuous
                    vv
clus                 DISTANT METASTASIS
  C10ORF54 MUTATED                    0
  C10ORF54 WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  C10ORF54 MUTATED                                                                                          1
  C10ORF54 WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  C10ORF54 MUTATED                     3
  C10ORF54 WILD-TYPE                  10
D56V3, multiclass
                                                                                          clus
vv                                                                                         C10ORF54 MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         C10ORF54 WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                      10
D56V4, binary
                    cls
clus                  0  1
  C10ORF54 MUTATED    0  4
  C10ORF54 WILD-TYPE  8 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF54 MUTATED      0    4
  C10ORF54 WILD-TYPE    8   13
        clus
vv       C10ORF54 MUTATED C10ORF54 WILD-TYPE
  FEMALE                0                  8
  MALE                  4                 13
                    vv
clus                 N0 N1B N2C N3
  C10ORF54 MUTATED    2   1   1  0
  C10ORF54 WILD-TYPE 14   2   1  2
D56V5, multiclass
     clus
vv    C10ORF54 MUTATED C10ORF54 WILD-TYPE
  N0                 2                 14
  N1B                1                  2
  N2C                1                  1
  N3                 0                  2
D56V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  C10ORF54 MUTATED          1        0        0         1          2          0
  C10ORF54 WILD-TYPE        2        1        6         2          1          4
                    vv
clus                 STAGE IV
  C10ORF54 MUTATED          0
  C10ORF54 WILD-TYPE        1
D56V7, multiclass

Clustering(57) Variable = C10ORF120 MUTATION ANALYSIS
D57V1, survival
                     sevent
clus2                 0 1
  C10ORF120 MUTATED   0 2
  C10ORF120 WILD-TYPE 3 8
  C10ORF120 MUTATED C10ORF120 WILD-TYPE 
                  2                  11 
  C10ORF120 MUTATED C10ORF120 WILD-TYPE 
                  2                   8 
$`C10ORF120 MUTATED`
TCGA-EE-A181 TCGA-EE-A182 
        1.12         1.35 

$`C10ORF120 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29N 
       30.87        10.03         6.64        11.57         1.08         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        2.43        23.90        11.11         0.20        10.09 

  C10ORF120 MUTATED C10ORF120 WILD-TYPE 
               1.12                0.20 
  C10ORF120 MUTATED C10ORF120 WILD-TYPE 
               1.35               30.87 
  C10ORF120 MUTATED C10ORF120 WILD-TYPE 
              1.235              10.030 
[1] "1.1 - 1.4 (1.2)"   "0.2 - 30.9 (10.0)"
         TCGA-D3-A2JF          TCGA-DA-A1I0          TCGA-DA-A1IC 
"C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" 
         TCGA-EE-A17X          TCGA-EE-A181          TCGA-EE-A182 
"C10ORF120 WILD-TYPE"   "C10ORF120 MUTATED"   "C10ORF120 MUTATED" 
         TCGA-EE-A29L          TCGA-EE-A29N          TCGA-EE-A29V 
"C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" 
         TCGA-EE-A2A2          TCGA-ER-A19F          TCGA-FW-A3I3 
"C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" 
         TCGA-GN-A266 
"C10ORF120 WILD-TYPE" 
         TCGA-D3-A2JF          TCGA-DA-A1I0          TCGA-DA-A1IC 
"C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" 
         TCGA-EE-A17X          TCGA-EE-A181          TCGA-EE-A182 
"C10ORF120 WILD-TYPE"   "C10ORF120 MUTATED"   "C10ORF120 MUTATED" 
         TCGA-EE-A29L          TCGA-EE-A29N          TCGA-EE-A29V 
"C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" 
         TCGA-EE-A2A2          TCGA-ER-A19F          TCGA-FW-A3I3 
"C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" 
         TCGA-GN-A266 
"C10ORF120 WILD-TYPE" 
         TCGA-D3-A2JF          TCGA-DA-A1I0          TCGA-DA-A1IC 
"C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" 
         TCGA-EE-A17X          TCGA-EE-A181          TCGA-EE-A182 
"C10ORF120 WILD-TYPE"   "C10ORF120 MUTATED"   "C10ORF120 MUTATED" 
         TCGA-EE-A29L          TCGA-EE-A29N          TCGA-EE-A29V 
"C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" 
         TCGA-EE-A2A2          TCGA-ER-A19F          TCGA-FW-A3I3 
"C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" 
         TCGA-GN-A266 
"C10ORF120 WILD-TYPE" 
[1] "Remove cluster labels:" "C10ORF120 MUTATED"     
clus
  C10ORF120 MUTATED C10ORF120 WILD-TYPE 
                  2                  11 
         TCGA-D3-A2JF          TCGA-DA-A1I0          TCGA-DA-A1IC 
"C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" 
         TCGA-EE-A17X          TCGA-EE-A29L          TCGA-EE-A29N 
"C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" 
         TCGA-EE-A29V          TCGA-EE-A2A2          TCGA-ER-A19F 
"C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" 
         TCGA-FW-A3I3          TCGA-GN-A266 
"C10ORF120 WILD-TYPE" "C10ORF120 WILD-TYPE" 
D57V2, continuous
                     vv
clus                  DISTANT METASTASIS
  C10ORF120 MUTATED                    1
  C10ORF120 WILD-TYPE                  6
                     vv
clus                  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  C10ORF120 MUTATED                                                                                          0
  C10ORF120 WILD-TYPE                                                                                        5
                     vv
clus                  REGIONAL LYMPH NODE
  C10ORF120 MUTATED                     5
  C10ORF120 WILD-TYPE                   8
D57V3, multiclass
                                                                                          clus
vv                                                                                         C10ORF120 MUTATED
  DISTANT METASTASIS                                                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 0
  REGIONAL LYMPH NODE                                                                                      5
                                                                                          clus
vv                                                                                         C10ORF120 WILD-TYPE
  DISTANT METASTASIS                                                                                         6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                   5
  REGIONAL LYMPH NODE                                                                                        8
D57V4, binary
                     cls
clus                   0  1
  C10ORF120 MUTATED    3  3
  C10ORF120 WILD-TYPE  5 14
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF120 MUTATED      3    3
  C10ORF120 WILD-TYPE    5   14
        clus
vv       C10ORF120 MUTATED C10ORF120 WILD-TYPE
  FEMALE                 3                   5
  MALE                   3                  14
                     vv
clus                  N0 N1B N2C N3
  C10ORF120 MUTATED    5   1   0  0
  C10ORF120 WILD-TYPE 11   2   2  2
D57V5, multiclass
     clus
vv    C10ORF120 MUTATED C10ORF120 WILD-TYPE
  N0                  5                  11
  N1B                 1                   2
  N2C                 0                   2
  N3                  0                   2
D57V6, continuous
                     vv
clus                  STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB
  C10ORF120 MUTATED          1        0        3         1          0
  C10ORF120 WILD-TYPE        2        1        3         2          3
                     vv
clus                  STAGE IIIC STAGE IV
  C10ORF120 MUTATED            1        0
  C10ORF120 WILD-TYPE          3        1
D57V7, multiclass

Clustering(58) Variable = CHSY1 MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2             0 1
  CHSY1 MUTATED   0 2
  CHSY1 WILD-TYPE 3 8
  CHSY1 MUTATED CHSY1 WILD-TYPE 
              2              11 
  CHSY1 MUTATED CHSY1 WILD-TYPE 
              2               8 
$`CHSY1 MUTATED`
TCGA-EE-A182 TCGA-EE-A29L 
        1.35         1.08 

$`CHSY1 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29N 
       30.87        10.03         6.64        11.57         1.12         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        2.43        23.90        11.11         0.20        10.09 

  CHSY1 MUTATED CHSY1 WILD-TYPE 
           1.08            0.20 
  CHSY1 MUTATED CHSY1 WILD-TYPE 
           1.35           30.87 
  CHSY1 MUTATED CHSY1 WILD-TYPE 
          1.215          10.030 
[1] "1.1 - 1.4 (1.2)"   "0.2 - 30.9 (10.0)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"CHSY1 WILD-TYPE"   "CHSY1 MUTATED"   "CHSY1 MUTATED" "CHSY1 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" 
     TCGA-GN-A266 
"CHSY1 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"CHSY1 WILD-TYPE"   "CHSY1 MUTATED"   "CHSY1 MUTATED" "CHSY1 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" 
     TCGA-GN-A266 
"CHSY1 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"CHSY1 WILD-TYPE"   "CHSY1 MUTATED"   "CHSY1 MUTATED" "CHSY1 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" 
     TCGA-GN-A266 
"CHSY1 WILD-TYPE" 
[1] "Remove cluster labels:" "CHSY1 MUTATED"         
clus
  CHSY1 MUTATED CHSY1 WILD-TYPE 
              2              11 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A29N      TCGA-EE-A29V      TCGA-EE-A2A2 
"CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" 
     TCGA-ER-A19F      TCGA-FW-A3I3      TCGA-GN-A266 
"CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" "CHSY1 WILD-TYPE" 
D58V2, continuous
                 vv
clus              DISTANT METASTASIS
  CHSY1 MUTATED                    1
  CHSY1 WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CHSY1 MUTATED                                                                                          0
  CHSY1 WILD-TYPE                                                                                        5
                 vv
clus              REGIONAL LYMPH NODE
  CHSY1 MUTATED                     3
  CHSY1 WILD-TYPE                  10
D58V3, multiclass
                                                                                          clus
vv                                                                                         CHSY1 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         CHSY1 WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                   10
D58V4, binary
                 cls
clus               0  1
  CHSY1 MUTATED    1  3
  CHSY1 WILD-TYPE  7 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHSY1 MUTATED      1    3
  CHSY1 WILD-TYPE    7   14
        clus
vv       CHSY1 MUTATED CHSY1 WILD-TYPE
  FEMALE             1               7
  MALE               3              14
                 vv
clus              N0 N1B N2C N3
  CHSY1 MUTATED    2   1   0  1
  CHSY1 WILD-TYPE 14   2   2  1
D58V5, multiclass
     clus
vv    CHSY1 MUTATED CHSY1 WILD-TYPE
  N0              2              14
  N1B             1               2
  N2C             0               2
  N3              1               1
D58V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  CHSY1 MUTATED          0        1        1         0          0          2
  CHSY1 WILD-TYPE        3        0        5         3          3          2
                 vv
clus              STAGE IV
  CHSY1 MUTATED          0
  CHSY1 WILD-TYPE        1
D58V7, multiclass

Clustering(59) Variable = CSF2RA MUTATION ANALYSIS
D59V1, survival
                  sevent
clus2              0 1
  CSF2RA MUTATED   1 2
  CSF2RA WILD-TYPE 2 8
  CSF2RA MUTATED CSF2RA WILD-TYPE 
               3               10 
  CSF2RA MUTATED CSF2RA WILD-TYPE 
               2                8 
$`CSF2RA MUTATED`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A182 
       30.87         6.64         1.35 

$`CSF2RA WILD-TYPE`
TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V 
       10.03        11.57         1.12         1.08         9.47         2.43 
TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
       23.90        11.11         0.20        10.09 

  CSF2RA MUTATED CSF2RA WILD-TYPE 
            1.35             0.20 
  CSF2RA MUTATED CSF2RA WILD-TYPE 
           30.87            23.90 
  CSF2RA MUTATED CSF2RA WILD-TYPE 
            6.64             9.75 
[1] "1.4 - 30.9 (6.6)" "0.2 - 23.9 (9.8)"
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
  "CSF2RA MUTATED" "CSF2RA WILD-TYPE"   "CSF2RA MUTATED" "CSF2RA WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"CSF2RA WILD-TYPE"   "CSF2RA MUTATED" "CSF2RA WILD-TYPE" "CSF2RA WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"CSF2RA WILD-TYPE" "CSF2RA WILD-TYPE" "CSF2RA WILD-TYPE" "CSF2RA WILD-TYPE" 
      TCGA-GN-A266 
"CSF2RA WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
  "CSF2RA MUTATED" "CSF2RA WILD-TYPE"   "CSF2RA MUTATED" "CSF2RA WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"CSF2RA WILD-TYPE"   "CSF2RA MUTATED" "CSF2RA WILD-TYPE" "CSF2RA WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"CSF2RA WILD-TYPE" "CSF2RA WILD-TYPE" "CSF2RA WILD-TYPE" "CSF2RA WILD-TYPE" 
      TCGA-GN-A266 
"CSF2RA WILD-TYPE" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
  "CSF2RA MUTATED" "CSF2RA WILD-TYPE"   "CSF2RA MUTATED" "CSF2RA WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"CSF2RA WILD-TYPE"   "CSF2RA MUTATED" "CSF2RA WILD-TYPE" "CSF2RA WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"CSF2RA WILD-TYPE" "CSF2RA WILD-TYPE" "CSF2RA WILD-TYPE" "CSF2RA WILD-TYPE" 
      TCGA-GN-A266 
"CSF2RA WILD-TYPE" 
[1] "hr=" "1.3"
D59V2, continuous
                  vv
clus               DISTANT METASTASIS
  CSF2RA MUTATED                    3
  CSF2RA WILD-TYPE                  4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CSF2RA MUTATED                                                                                          1
  CSF2RA WILD-TYPE                                                                                        4
                  vv
clus               REGIONAL LYMPH NODE
  CSF2RA MUTATED                     2
  CSF2RA WILD-TYPE                  11
D59V3, multiclass
                                                                                          clus
vv                                                                                         CSF2RA MUTATED
  DISTANT METASTASIS                                                                                    3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   2
                                                                                          clus
vv                                                                                         CSF2RA WILD-TYPE
  DISTANT METASTASIS                                                                                      4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                    11
D59V4, binary
                  cls
clus                0  1
  CSF2RA MUTATED    2  4
  CSF2RA WILD-TYPE  6 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSF2RA MUTATED      2    4
  CSF2RA WILD-TYPE    6   13
        clus
vv       CSF2RA MUTATED CSF2RA WILD-TYPE
  FEMALE              2                6
  MALE                4               13
                  vv
clus               N0 N1B N2C N3
  CSF2RA MUTATED    4   1   1  0
  CSF2RA WILD-TYPE 12   2   1  2
D59V5, multiclass
     clus
vv    CSF2RA MUTATED CSF2RA WILD-TYPE
  N0               4               12
  N1B              1                2
  N2C              1                1
  N3               0                2
D59V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  CSF2RA MUTATED          1        0        0         3          1          1
  CSF2RA WILD-TYPE        2        1        6         0          2          3
                  vv
clus               STAGE IV
  CSF2RA MUTATED          0
  CSF2RA WILD-TYPE        1
D59V7, multiclass

Clustering(60) Variable = KCND2 MUTATION ANALYSIS
D60V1, survival
                 sevent
clus2             0 1
  KCND2 MUTATED   1 3
  KCND2 WILD-TYPE 2 7
  KCND2 MUTATED KCND2 WILD-TYPE 
              4               9 
  KCND2 MUTATED KCND2 WILD-TYPE 
              3               7 
$`KCND2 MUTATED`
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A2A2 TCGA-GN-A266 
        1.12         1.35        23.90        10.09 

$`KCND2 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29N 
       30.87        10.03         6.64        11.57         1.08         9.47 
TCGA-EE-A29V TCGA-ER-A19F TCGA-FW-A3I3 
        2.43        11.11         0.20 

  KCND2 MUTATED KCND2 WILD-TYPE 
           1.12            0.20 
  KCND2 MUTATED KCND2 WILD-TYPE 
          23.90           30.87 
  KCND2 MUTATED KCND2 WILD-TYPE 
           5.72            9.47 
[1] "1.1 - 23.9 (5.7)" "0.2 - 30.9 (9.5)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"KCND2 WILD-TYPE" "KCND2 WILD-TYPE" "KCND2 WILD-TYPE" "KCND2 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "KCND2 MUTATED"   "KCND2 MUTATED" "KCND2 WILD-TYPE" "KCND2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"KCND2 WILD-TYPE"   "KCND2 MUTATED" "KCND2 WILD-TYPE" "KCND2 WILD-TYPE" 
     TCGA-GN-A266 
  "KCND2 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"KCND2 WILD-TYPE" "KCND2 WILD-TYPE" "KCND2 WILD-TYPE" "KCND2 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "KCND2 MUTATED"   "KCND2 MUTATED" "KCND2 WILD-TYPE" "KCND2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"KCND2 WILD-TYPE"   "KCND2 MUTATED" "KCND2 WILD-TYPE" "KCND2 WILD-TYPE" 
     TCGA-GN-A266 
  "KCND2 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"KCND2 WILD-TYPE" "KCND2 WILD-TYPE" "KCND2 WILD-TYPE" "KCND2 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "KCND2 MUTATED"   "KCND2 MUTATED" "KCND2 WILD-TYPE" "KCND2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"KCND2 WILD-TYPE"   "KCND2 MUTATED" "KCND2 WILD-TYPE" "KCND2 WILD-TYPE" 
     TCGA-GN-A266 
  "KCND2 MUTATED" 
[1] "hr=" "1"  
D60V2, continuous
                 vv
clus              DISTANT METASTASIS
  KCND2 MUTATED                    2
  KCND2 WILD-TYPE                  5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  KCND2 MUTATED                                                                                          3
  KCND2 WILD-TYPE                                                                                        2
                 vv
clus              REGIONAL LYMPH NODE
  KCND2 MUTATED                     3
  KCND2 WILD-TYPE                  10
D60V3, multiclass
                                                                                          clus
vv                                                                                         KCND2 MUTATED
  DISTANT METASTASIS                                                                                   2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             3
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         KCND2 WILD-TYPE
  DISTANT METASTASIS                                                                                     5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                   10
D60V4, binary
                 cls
clus               0  1
  KCND2 MUTATED    4  4
  KCND2 WILD-TYPE  4 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCND2 MUTATED      4    4
  KCND2 WILD-TYPE    4   13
        clus
vv       KCND2 MUTATED KCND2 WILD-TYPE
  FEMALE             4               4
  MALE               4              13
                 vv
clus              N0 N1B N2C N3
  KCND2 MUTATED    4   2   0  0
  KCND2 WILD-TYPE 12   1   2  2
D60V5, multiclass
     clus
vv    KCND2 MUTATED KCND2 WILD-TYPE
  N0              4              12
  N1B             2               1
  N2C             0               2
  N3              0               2
D60V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  KCND2 MUTATED          0        0        3         1          1          1
  KCND2 WILD-TYPE        3        1        3         2          2          3
                 vv
clus              STAGE IV
  KCND2 MUTATED          0
  KCND2 WILD-TYPE        1
D60V7, multiclass

Clustering(61) Variable = SPEF2 MUTATION ANALYSIS
D61V1, survival
                 sevent
clus2             0 1
  SPEF2 MUTATED   1 6
  SPEF2 WILD-TYPE 2 4
  SPEF2 MUTATED SPEF2 WILD-TYPE 
              7               6 
  SPEF2 MUTATED SPEF2 WILD-TYPE 
              6               4 
$`SPEF2 MUTATED`
TCGA-D3-A2JF TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
       30.87        11.57         1.12         1.35         1.08         9.47 
TCGA-GN-A266 
       10.09 

$`SPEF2 WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 
       10.03         6.64         2.43        23.90        11.11         0.20 

  SPEF2 MUTATED SPEF2 WILD-TYPE 
           1.08            0.20 
  SPEF2 MUTATED SPEF2 WILD-TYPE 
          30.87           23.90 
  SPEF2 MUTATED SPEF2 WILD-TYPE 
          9.470           8.335 
[1] "1.1 - 30.9 (9.5)" "0.2 - 23.9 (8.3)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "SPEF2 MUTATED" "SPEF2 WILD-TYPE" "SPEF2 WILD-TYPE"   "SPEF2 MUTATED" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "SPEF2 MUTATED"   "SPEF2 MUTATED"   "SPEF2 MUTATED"   "SPEF2 MUTATED" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"SPEF2 WILD-TYPE" "SPEF2 WILD-TYPE" "SPEF2 WILD-TYPE" "SPEF2 WILD-TYPE" 
     TCGA-GN-A266 
  "SPEF2 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "SPEF2 MUTATED" "SPEF2 WILD-TYPE" "SPEF2 WILD-TYPE"   "SPEF2 MUTATED" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "SPEF2 MUTATED"   "SPEF2 MUTATED"   "SPEF2 MUTATED"   "SPEF2 MUTATED" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"SPEF2 WILD-TYPE" "SPEF2 WILD-TYPE" "SPEF2 WILD-TYPE" "SPEF2 WILD-TYPE" 
     TCGA-GN-A266 
  "SPEF2 MUTATED" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "SPEF2 MUTATED" "SPEF2 WILD-TYPE" "SPEF2 WILD-TYPE"   "SPEF2 MUTATED" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
  "SPEF2 MUTATED"   "SPEF2 MUTATED"   "SPEF2 MUTATED"   "SPEF2 MUTATED" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"SPEF2 WILD-TYPE" "SPEF2 WILD-TYPE" "SPEF2 WILD-TYPE" "SPEF2 WILD-TYPE" 
     TCGA-GN-A266 
  "SPEF2 MUTATED" 
[1] "hr=" "1.3"
D61V2, continuous
                 vv
clus              DISTANT METASTASIS
  SPEF2 MUTATED                    3
  SPEF2 WILD-TYPE                  4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  SPEF2 MUTATED                                                                                          2
  SPEF2 WILD-TYPE                                                                                        3
                 vv
clus              REGIONAL LYMPH NODE
  SPEF2 MUTATED                     6
  SPEF2 WILD-TYPE                   7
D61V3, multiclass
                                                                                          clus
vv                                                                                         SPEF2 MUTATED
  DISTANT METASTASIS                                                                                   3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  6
                                                                                          clus
vv                                                                                         SPEF2 WILD-TYPE
  DISTANT METASTASIS                                                                                     4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    7
D61V4, binary
                 cls
clus               0  1
  SPEF2 MUTATED    5  6
  SPEF2 WILD-TYPE  3 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPEF2 MUTATED      5    6
  SPEF2 WILD-TYPE    3   11
        clus
vv       SPEF2 MUTATED SPEF2 WILD-TYPE
  FEMALE             5               3
  MALE               6              11
                 vv
clus              N0 N1B N2C N3
  SPEF2 MUTATED    8   1   0  1
  SPEF2 WILD-TYPE  8   2   2  1
D61V5, multiclass
     clus
vv    SPEF2 MUTATED SPEF2 WILD-TYPE
  N0              8               8
  N1B             1               2
  N2C             0               2
  N3              1               1
D61V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  SPEF2 MUTATED          3        0        3         1          0          2
  SPEF2 WILD-TYPE        0        1        3         2          3          2
                 vv
clus              STAGE IV
  SPEF2 MUTATED          0
  SPEF2 WILD-TYPE        1
D61V7, multiclass

Clustering(62) Variable = RPGRIP1 MUTATION ANALYSIS
D62V1, survival
                   sevent
clus2               0 1
  RPGRIP1 MUTATED   0 1
  RPGRIP1 WILD-TYPE 3 9
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
                1                12 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
                1                 9 
$`RPGRIP1 MUTATED`
TCGA-DA-A1IC 
        6.64 

$`RPGRIP1 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L 
       30.87        10.03        11.57         1.12         1.35         1.08 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        9.47         2.43        23.90        11.11         0.20        10.09 

  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
             6.64              0.20 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
             6.64             30.87 
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
             6.64              9.75 
[1] "6.6 - 6.6 (6.6)"  "0.2 - 30.9 (9.8)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE"   "RPGRIP1 MUTATED" "RPGRIP1 WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-GN-A266 
"RPGRIP1 WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE"   "RPGRIP1 MUTATED" "RPGRIP1 WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-GN-A266 
"RPGRIP1 WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE"   "RPGRIP1 MUTATED" "RPGRIP1 WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-GN-A266 
"RPGRIP1 WILD-TYPE" 
[1] "Remove cluster labels:" "RPGRIP1 MUTATED"       
clus
  RPGRIP1 MUTATED RPGRIP1 WILD-TYPE 
                1                12 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-EE-A17X        TCGA-EE-A181 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29V 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3        TCGA-GN-A266 
"RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" "RPGRIP1 WILD-TYPE" 
D62V2, continuous
                   vv
clus                DISTANT METASTASIS
  RPGRIP1 MUTATED                    0
  RPGRIP1 WILD-TYPE                  7
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  RPGRIP1 MUTATED                                                                                          1
  RPGRIP1 WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  RPGRIP1 MUTATED                     5
  RPGRIP1 WILD-TYPE                   8
D62V3, multiclass
                                                                                          clus
vv                                                                                         RPGRIP1 MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         RPGRIP1 WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                      8
D62V4, binary
                   cls
clus                 0  1
  RPGRIP1 MUTATED    0  6
  RPGRIP1 WILD-TYPE  8 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPGRIP1 MUTATED      0    6
  RPGRIP1 WILD-TYPE    8   11
        clus
vv       RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  FEMALE               0                 8
  MALE                 6                11
                   vv
clus                N0 N1B N2C N3
  RPGRIP1 MUTATED    5   0   1  0
  RPGRIP1 WILD-TYPE 11   3   1  2
D62V5, multiclass
     clus
vv    RPGRIP1 MUTATED RPGRIP1 WILD-TYPE
  N0                5                11
  N1B               0                 3
  N2C               1                 1
  N3                0                 2
D62V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  RPGRIP1 MUTATED          0        1        2         2          1          0
  RPGRIP1 WILD-TYPE        3        0        4         1          2          4
                   vv
clus                STAGE IV
  RPGRIP1 MUTATED          0
  RPGRIP1 WILD-TYPE        1
D62V7, multiclass

Clustering(63) Variable = OR2L3 MUTATION ANALYSIS
D63V1, survival
                 sevent
clus2             0 1
  OR2L3 MUTATED   0 1
  OR2L3 WILD-TYPE 3 9
  OR2L3 MUTATED OR2L3 WILD-TYPE 
              1              12 
  OR2L3 MUTATED OR2L3 WILD-TYPE 
              1               9 
$`OR2L3 MUTATED`
TCGA-DA-A1I0 
       10.03 

$`OR2L3 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L 
       30.87         6.64        11.57         1.12         1.35         1.08 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        9.47         2.43        23.90        11.11         0.20        10.09 

  OR2L3 MUTATED OR2L3 WILD-TYPE 
          10.03            0.20 
  OR2L3 MUTATED OR2L3 WILD-TYPE 
          10.03           30.87 
  OR2L3 MUTATED OR2L3 WILD-TYPE 
         10.030           8.055 
[1] "10.0 - 10.0 (10.0)" "0.2 - 30.9 (8.1)"  
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"OR2L3 WILD-TYPE"   "OR2L3 MUTATED" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" 
     TCGA-GN-A266 
"OR2L3 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"OR2L3 WILD-TYPE"   "OR2L3 MUTATED" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" 
     TCGA-GN-A266 
"OR2L3 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"OR2L3 WILD-TYPE"   "OR2L3 MUTATED" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" 
     TCGA-GN-A266 
"OR2L3 WILD-TYPE" 
[1] "Remove cluster labels:" "OR2L3 MUTATED"         
clus
  OR2L3 MUTATED OR2L3 WILD-TYPE 
              1              12 
     TCGA-D3-A2JF      TCGA-DA-A1IC      TCGA-EE-A17X      TCGA-EE-A181 
"OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" 
     TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N      TCGA-EE-A29V 
"OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3      TCGA-GN-A266 
"OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" "OR2L3 WILD-TYPE" 
D63V2, continuous
                 vv
clus              DISTANT METASTASIS
  OR2L3 MUTATED                    1
  OR2L3 WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  OR2L3 MUTATED                                                                                          1
  OR2L3 WILD-TYPE                                                                                        4
                 vv
clus              REGIONAL LYMPH NODE
  OR2L3 MUTATED                     1
  OR2L3 WILD-TYPE                  12
D63V3, multiclass
                                                                                          clus
vv                                                                                         OR2L3 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  1
                                                                                          clus
vv                                                                                         OR2L3 WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                   12
D63V4, binary
                 cls
clus               0  1
  OR2L3 MUTATED    1  2
  OR2L3 WILD-TYPE  7 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2L3 MUTATED      1    2
  OR2L3 WILD-TYPE    7   15
        clus
vv       OR2L3 MUTATED OR2L3 WILD-TYPE
  FEMALE             1               7
  MALE               2              15
                 vv
clus              N0 N1B N2C N3
  OR2L3 MUTATED    2   0   0  1
  OR2L3 WILD-TYPE 14   3   2  1
D63V5, multiclass
     clus
vv    OR2L3 MUTATED OR2L3 WILD-TYPE
  N0              2              14
  N1B             0               3
  N2C             0               2
  N3              1               1
D63V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  OR2L3 MUTATED          0        0        1         1          0          1
  OR2L3 WILD-TYPE        3        1        5         2          3          3
                 vv
clus              STAGE IV
  OR2L3 MUTATED          0
  OR2L3 WILD-TYPE        1
D63V7, multiclass

Clustering(64) Variable = CCDC54 MUTATION ANALYSIS
D64V1, survival
                  sevent
clus2              0 1
  CCDC54 MUTATED   0 3
  CCDC54 WILD-TYPE 3 7
  CCDC54 MUTATED CCDC54 WILD-TYPE 
               3               10 
  CCDC54 MUTATED CCDC54 WILD-TYPE 
               3                7 
$`CCDC54 MUTATED`
TCGA-EE-A29N TCGA-ER-A19F TCGA-GN-A266 
        9.47        11.11        10.09 

$`CCDC54 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       30.87        10.03         6.64        11.57         1.12         1.35 
TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A2A2 TCGA-FW-A3I3 
        1.08         2.43        23.90         0.20 

  CCDC54 MUTATED CCDC54 WILD-TYPE 
            9.47             0.20 
  CCDC54 MUTATED CCDC54 WILD-TYPE 
           11.11            30.87 
  CCDC54 MUTATED CCDC54 WILD-TYPE 
          10.090            4.535 
[1] "9.5 - 11.1 (10.1)" "0.2 - 30.9 (4.5)" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE"   "CCDC54 MUTATED" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE"   "CCDC54 MUTATED" "CCDC54 WILD-TYPE" 
      TCGA-GN-A266 
  "CCDC54 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE"   "CCDC54 MUTATED" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE"   "CCDC54 MUTATED" "CCDC54 WILD-TYPE" 
      TCGA-GN-A266 
  "CCDC54 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE"   "CCDC54 MUTATED" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE"   "CCDC54 MUTATED" "CCDC54 WILD-TYPE" 
      TCGA-GN-A266 
  "CCDC54 MUTATED" 
[1] "hr=" "1"  
D64V2, continuous
                  vv
clus               DISTANT METASTASIS
  CCDC54 MUTATED                    0
  CCDC54 WILD-TYPE                  7
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CCDC54 MUTATED                                                                                          1
  CCDC54 WILD-TYPE                                                                                        4
                  vv
clus               REGIONAL LYMPH NODE
  CCDC54 MUTATED                     4
  CCDC54 WILD-TYPE                   9
D64V3, multiclass
                                                                                          clus
vv                                                                                         CCDC54 MUTATED
  DISTANT METASTASIS                                                                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   4
                                                                                          clus
vv                                                                                         CCDC54 WILD-TYPE
  DISTANT METASTASIS                                                                                      7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                     9
D64V4, binary
                  cls
clus                0  1
  CCDC54 MUTATED    1  4
  CCDC54 WILD-TYPE  7 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC54 MUTATED      1    4
  CCDC54 WILD-TYPE    7   13
        clus
vv       CCDC54 MUTATED CCDC54 WILD-TYPE
  FEMALE              1                7
  MALE                4               13
                  vv
clus               N0 N1B N2C N3
  CCDC54 MUTATED    4   0   0  0
  CCDC54 WILD-TYPE 12   3   2  2
D64V5, multiclass
     clus
vv    CCDC54 MUTATED CCDC54 WILD-TYPE
  N0               4               12
  N1B              0                3
  N2C              0                2
  N3               0                2
D64V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  CCDC54 MUTATED          1        0        0         1          0          0
  CCDC54 WILD-TYPE        2        1        6         2          3          4
                  vv
clus               STAGE IV
  CCDC54 MUTATED          0
  CCDC54 WILD-TYPE        1
D64V7, multiclass
[1] "Remove cluster labels:" "CCDC54 MUTATED"        
clus
  CCDC54 MUTATED CCDC54 WILD-TYPE 
               2               19 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29V 
"CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2GO       TCGA-EE-A2GR       TCGA-EE-A2MI 
"CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" 
      TCGA-EE-A2MJ       TCGA-EE-A2MS       TCGA-EE-A2MT       TCGA-FS-A1ZA 
"CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" 
      TCGA-FS-A1ZP       TCGA-FS-A1ZZ       TCGA-FW-A3I3 
"CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" "CCDC54 WILD-TYPE" 

Clustering(65) Variable = KLHL14 MUTATION ANALYSIS
D65V1, survival
                  sevent
clus2              0 1
  KLHL14 MUTATED   1 3
  KLHL14 WILD-TYPE 2 7
  KLHL14 MUTATED KLHL14 WILD-TYPE 
               4                9 
  KLHL14 MUTATED KLHL14 WILD-TYPE 
               3                7 
$`KLHL14 MUTATED`
TCGA-EE-A182 TCGA-EE-A2A2 TCGA-ER-A19F TCGA-GN-A266 
        1.35        23.90        11.11        10.09 

$`KLHL14 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29L 
       30.87        10.03         6.64        11.57         1.12         1.08 
TCGA-EE-A29N TCGA-EE-A29V TCGA-FW-A3I3 
        9.47         2.43         0.20 

  KLHL14 MUTATED KLHL14 WILD-TYPE 
            1.35             0.20 
  KLHL14 MUTATED KLHL14 WILD-TYPE 
           23.90            30.87 
  KLHL14 MUTATED KLHL14 WILD-TYPE 
           10.60             6.64 
[1] "1.4 - 23.9 (10.6)" "0.2 - 30.9 (6.6)" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"KLHL14 WILD-TYPE"   "KLHL14 MUTATED" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"KLHL14 WILD-TYPE"   "KLHL14 MUTATED"   "KLHL14 MUTATED" "KLHL14 WILD-TYPE" 
      TCGA-GN-A266 
  "KLHL14 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"KLHL14 WILD-TYPE"   "KLHL14 MUTATED" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"KLHL14 WILD-TYPE"   "KLHL14 MUTATED"   "KLHL14 MUTATED" "KLHL14 WILD-TYPE" 
      TCGA-GN-A266 
  "KLHL14 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"KLHL14 WILD-TYPE"   "KLHL14 MUTATED" "KLHL14 WILD-TYPE" "KLHL14 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"KLHL14 WILD-TYPE"   "KLHL14 MUTATED"   "KLHL14 MUTATED" "KLHL14 WILD-TYPE" 
      TCGA-GN-A266 
  "KLHL14 MUTATED" 
[1] "hr=" "1.7"
D65V2, continuous
                  vv
clus               DISTANT METASTASIS
  KLHL14 MUTATED                    1
  KLHL14 WILD-TYPE                  6
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  KLHL14 MUTATED                                                                                          1
  KLHL14 WILD-TYPE                                                                                        4
                  vv
clus               REGIONAL LYMPH NODE
  KLHL14 MUTATED                     3
  KLHL14 WILD-TYPE                  10
D65V3, multiclass
                                                                                          clus
vv                                                                                         KLHL14 MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   3
                                                                                          clus
vv                                                                                         KLHL14 WILD-TYPE
  DISTANT METASTASIS                                                                                      6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                    10
D65V4, binary
                  cls
clus                0  1
  KLHL14 MUTATED    1  4
  KLHL14 WILD-TYPE  7 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL14 MUTATED      1    4
  KLHL14 WILD-TYPE    7   13
        clus
vv       KLHL14 MUTATED KLHL14 WILD-TYPE
  FEMALE              1                7
  MALE                4               13
                  vv
clus               N0 N1B N2C N3
  KLHL14 MUTATED    2   2   0  0
  KLHL14 WILD-TYPE 14   1   2  2
D65V5, multiclass
     clus
vv    KLHL14 MUTATED KLHL14 WILD-TYPE
  N0               2               14
  N1B              2                1
  N2C              0                2
  N3               0                2
D65V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  KLHL14 MUTATED          0        0        1         0          1          1
  KLHL14 WILD-TYPE        3        1        5         3          2          3
                  vv
clus               STAGE IV
  KLHL14 MUTATED          0
  KLHL14 WILD-TYPE        1
D65V7, multiclass

Clustering(66) Variable = ZFX MUTATION ANALYSIS
D66V1, survival
               sevent
clus2           0 1
  ZFX MUTATED   1 1
  ZFX WILD-TYPE 2 9
  ZFX MUTATED ZFX WILD-TYPE 
            2            11 
  ZFX MUTATED ZFX WILD-TYPE 
            1             9 
$`ZFX MUTATED`
TCGA-D3-A2JF TCGA-DA-A1I0 
       30.87        10.03 

$`ZFX WILD-TYPE`
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
        6.64        11.57         1.12         1.35         1.08         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        2.43        23.90        11.11         0.20        10.09 

  ZFX MUTATED ZFX WILD-TYPE 
        10.03          0.20 
  ZFX MUTATED ZFX WILD-TYPE 
        30.87         23.90 
  ZFX MUTATED ZFX WILD-TYPE 
        20.45          6.64 
[1] "10.0 - 30.9 (20.4)" "0.2 - 23.9 (6.6)"  
   TCGA-D3-A2JF    TCGA-DA-A1I0    TCGA-DA-A1IC    TCGA-EE-A17X    TCGA-EE-A181 
  "ZFX MUTATED"   "ZFX MUTATED" "ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" 
   TCGA-EE-A182    TCGA-EE-A29L    TCGA-EE-A29N    TCGA-EE-A29V    TCGA-EE-A2A2 
"ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" 
   TCGA-ER-A19F    TCGA-FW-A3I3    TCGA-GN-A266 
"ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" 
   TCGA-D3-A2JF    TCGA-DA-A1I0    TCGA-DA-A1IC    TCGA-EE-A17X    TCGA-EE-A181 
  "ZFX MUTATED"   "ZFX MUTATED" "ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" 
   TCGA-EE-A182    TCGA-EE-A29L    TCGA-EE-A29N    TCGA-EE-A29V    TCGA-EE-A2A2 
"ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" 
   TCGA-ER-A19F    TCGA-FW-A3I3    TCGA-GN-A266 
"ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" 
   TCGA-D3-A2JF    TCGA-DA-A1I0    TCGA-DA-A1IC    TCGA-EE-A17X    TCGA-EE-A181 
  "ZFX MUTATED"   "ZFX MUTATED" "ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" 
   TCGA-EE-A182    TCGA-EE-A29L    TCGA-EE-A29N    TCGA-EE-A29V    TCGA-EE-A2A2 
"ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" 
   TCGA-ER-A19F    TCGA-FW-A3I3    TCGA-GN-A266 
"ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" 
[1] "Remove cluster labels:" "ZFX MUTATED"           
clus
  ZFX MUTATED ZFX WILD-TYPE 
            2            11 
   TCGA-DA-A1IC    TCGA-EE-A17X    TCGA-EE-A181    TCGA-EE-A182    TCGA-EE-A29L 
"ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" 
   TCGA-EE-A29N    TCGA-EE-A29V    TCGA-EE-A2A2    TCGA-ER-A19F    TCGA-FW-A3I3 
"ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" "ZFX WILD-TYPE" 
   TCGA-GN-A266 
"ZFX WILD-TYPE" 
D66V2, continuous
               vv
clus            DISTANT METASTASIS
  ZFX MUTATED                    2
  ZFX WILD-TYPE                  5
               vv
clus            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ZFX MUTATED                                                                                          3
  ZFX WILD-TYPE                                                                                        2
               vv
clus            REGIONAL LYMPH NODE
  ZFX MUTATED                     2
  ZFX WILD-TYPE                  11
D66V3, multiclass
                                                                                          clus
vv                                                                                         ZFX MUTATED
  DISTANT METASTASIS                                                                                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)           3
  REGIONAL LYMPH NODE                                                                                2
                                                                                          clus
vv                                                                                         ZFX WILD-TYPE
  DISTANT METASTASIS                                                                                   5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                 11
D66V4, binary
               cls
clus             0  1
  ZFX MUTATED    2  5
  ZFX WILD-TYPE  6 12
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      2    5
  ZFX WILD-TYPE    6   12
        clus
vv       ZFX MUTATED ZFX WILD-TYPE
  FEMALE           2             6
  MALE             5            12
               vv
clus            N0 N1B N2C N3
  ZFX MUTATED    6   0   0  1
  ZFX WILD-TYPE 10   3   2  1
D66V5, multiclass
     clus
vv    ZFX MUTATED ZFX WILD-TYPE
  N0            6            10
  N1B           0             3
  N2C           0             2
  N3            1             1
D66V6, continuous
               vv
clus            STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  ZFX MUTATED          1        0        3         2          0          1
  ZFX WILD-TYPE        2        1        3         1          3          3
               vv
clus            STAGE IV
  ZFX MUTATED          0
  ZFX WILD-TYPE        1
D66V7, multiclass

Clustering(67) Variable = KLHL13 MUTATION ANALYSIS
D67V1, survival
                  sevent
clus2              0 1
  KLHL13 MUTATED   0 5
  KLHL13 WILD-TYPE 3 5
  KLHL13 MUTATED KLHL13 WILD-TYPE 
               5                8 
  KLHL13 MUTATED KLHL13 WILD-TYPE 
               5                5 
$`KLHL13 MUTATED`
TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29N TCGA-ER-A19F TCGA-GN-A266 
       11.57         1.35         9.47        11.11        10.09 

$`KLHL13 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29V 
       30.87        10.03         6.64         1.12         1.08         2.43 
TCGA-EE-A2A2 TCGA-FW-A3I3 
       23.90         0.20 

  KLHL13 MUTATED KLHL13 WILD-TYPE 
            1.35             0.20 
  KLHL13 MUTATED KLHL13 WILD-TYPE 
           11.57            30.87 
  KLHL13 MUTATED KLHL13 WILD-TYPE 
          10.090            4.535 
[1] "1.4 - 11.6 (10.1)" "0.2 - 30.9 (4.5)" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"KLHL13 WILD-TYPE" "KLHL13 WILD-TYPE" "KLHL13 WILD-TYPE"   "KLHL13 MUTATED" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"KLHL13 WILD-TYPE"   "KLHL13 MUTATED" "KLHL13 WILD-TYPE"   "KLHL13 MUTATED" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"KLHL13 WILD-TYPE" "KLHL13 WILD-TYPE"   "KLHL13 MUTATED" "KLHL13 WILD-TYPE" 
      TCGA-GN-A266 
  "KLHL13 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"KLHL13 WILD-TYPE" "KLHL13 WILD-TYPE" "KLHL13 WILD-TYPE"   "KLHL13 MUTATED" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"KLHL13 WILD-TYPE"   "KLHL13 MUTATED" "KLHL13 WILD-TYPE"   "KLHL13 MUTATED" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"KLHL13 WILD-TYPE" "KLHL13 WILD-TYPE"   "KLHL13 MUTATED" "KLHL13 WILD-TYPE" 
      TCGA-GN-A266 
  "KLHL13 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"KLHL13 WILD-TYPE" "KLHL13 WILD-TYPE" "KLHL13 WILD-TYPE"   "KLHL13 MUTATED" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"KLHL13 WILD-TYPE"   "KLHL13 MUTATED" "KLHL13 WILD-TYPE"   "KLHL13 MUTATED" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"KLHL13 WILD-TYPE" "KLHL13 WILD-TYPE"   "KLHL13 MUTATED" "KLHL13 WILD-TYPE" 
      TCGA-GN-A266 
  "KLHL13 MUTATED" 
[1] "hr=" "1.1"
D67V2, continuous
                  vv
clus               DISTANT METASTASIS
  KLHL13 MUTATED                    3
  KLHL13 WILD-TYPE                  4
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  KLHL13 MUTATED                                                                                          2
  KLHL13 WILD-TYPE                                                                                        3
                  vv
clus               REGIONAL LYMPH NODE
  KLHL13 MUTATED                     5
  KLHL13 WILD-TYPE                   8
D67V3, multiclass
                                                                                          clus
vv                                                                                         KLHL13 MUTATED
  DISTANT METASTASIS                                                                                    3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              2
  REGIONAL LYMPH NODE                                                                                   5
                                                                                          clus
vv                                                                                         KLHL13 WILD-TYPE
  DISTANT METASTASIS                                                                                      4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     8
D67V4, binary
                  cls
clus                0  1
  KLHL13 MUTATED    5  5
  KLHL13 WILD-TYPE  3 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL13 MUTATED      5    5
  KLHL13 WILD-TYPE    3   12
        clus
vv       KLHL13 MUTATED KLHL13 WILD-TYPE
  FEMALE              5                3
  MALE                5               12
                  vv
clus               N0 N1B N2C N3
  KLHL13 MUTATED    6   1   1  0
  KLHL13 WILD-TYPE 10   2   1  2
D67V5, multiclass
     clus
vv    KLHL13 MUTATED KLHL13 WILD-TYPE
  N0               6               10
  N1B              1                2
  N2C              1                1
  N3               0                2
D67V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  KLHL13 MUTATED          2        0        1         1          1          1
  KLHL13 WILD-TYPE        1        1        5         2          2          3
                  vv
clus               STAGE IV
  KLHL13 MUTATED          0
  KLHL13 WILD-TYPE        1
D67V7, multiclass

Clustering(68) Variable = NSUN7 MUTATION ANALYSIS
D68V1, survival
                 sevent
clus2             0 1
  NSUN7 MUTATED   1 1
  NSUN7 WILD-TYPE 2 9
  NSUN7 MUTATED NSUN7 WILD-TYPE 
              2              11 
  NSUN7 MUTATED NSUN7 WILD-TYPE 
              1               9 
$`NSUN7 MUTATED`
TCGA-D3-A2JF TCGA-EE-A182 
       30.87         1.35 

$`NSUN7 WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29N 
       10.03         6.64        11.57         1.12         1.08         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        2.43        23.90        11.11         0.20        10.09 

  NSUN7 MUTATED NSUN7 WILD-TYPE 
           1.35            0.20 
  NSUN7 MUTATED NSUN7 WILD-TYPE 
          30.87           23.90 
  NSUN7 MUTATED NSUN7 WILD-TYPE 
          16.11            9.47 
[1] "1.4 - 30.9 (16.1)" "0.2 - 23.9 (9.5)" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "NSUN7 MUTATED" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"NSUN7 WILD-TYPE"   "NSUN7 MUTATED" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" 
     TCGA-GN-A266 
"NSUN7 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "NSUN7 MUTATED" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"NSUN7 WILD-TYPE"   "NSUN7 MUTATED" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" 
     TCGA-GN-A266 
"NSUN7 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "NSUN7 MUTATED" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"NSUN7 WILD-TYPE"   "NSUN7 MUTATED" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" 
     TCGA-GN-A266 
"NSUN7 WILD-TYPE" 
[1] "Remove cluster labels:" "NSUN7 MUTATED"         
clus
  NSUN7 MUTATED NSUN7 WILD-TYPE 
              2              11 
     TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X      TCGA-EE-A181 
"NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" 
     TCGA-EE-A29L      TCGA-EE-A29N      TCGA-EE-A29V      TCGA-EE-A2A2 
"NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" 
     TCGA-ER-A19F      TCGA-FW-A3I3      TCGA-GN-A266 
"NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" "NSUN7 WILD-TYPE" 
D68V2, continuous
                 vv
clus              DISTANT METASTASIS
  NSUN7 MUTATED                    2
  NSUN7 WILD-TYPE                  5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  NSUN7 MUTATED                                                                                          0
  NSUN7 WILD-TYPE                                                                                        5
                 vv
clus              REGIONAL LYMPH NODE
  NSUN7 MUTATED                     1
  NSUN7 WILD-TYPE                  12
D68V3, multiclass
                                                                                          clus
vv                                                                                         NSUN7 MUTATED
  DISTANT METASTASIS                                                                                   2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
  REGIONAL LYMPH NODE                                                                                  1
                                                                                          clus
vv                                                                                         NSUN7 WILD-TYPE
  DISTANT METASTASIS                                                                                     5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                   12
D68V4, binary
                 cls
clus               0  1
  NSUN7 MUTATED    1  2
  NSUN7 WILD-TYPE  7 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN7 MUTATED      1    2
  NSUN7 WILD-TYPE    7   15
        clus
vv       NSUN7 MUTATED NSUN7 WILD-TYPE
  FEMALE             1               7
  MALE               2              15
                 vv
clus              N0 N1B N2C N3
  NSUN7 MUTATED    2   1   0  0
  NSUN7 WILD-TYPE 14   2   2  2
D68V5, multiclass
     clus
vv    NSUN7 MUTATED NSUN7 WILD-TYPE
  N0              2              14
  N1B             1               2
  N2C             0               2
  N3              0               2
D68V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  NSUN7 MUTATED          1        0        1         0          0          1
  NSUN7 WILD-TYPE        2        1        5         3          3          3
                 vv
clus              STAGE IV
  NSUN7 MUTATED          0
  NSUN7 WILD-TYPE        1
D68V7, multiclass

Clustering(69) Variable = VEGFC MUTATION ANALYSIS
D69V1, survival
                 sevent
clus2              0  1
  VEGFC WILD-TYPE  3 10
VEGFC WILD-TYPE 
             13 
[1] 10
$`VEGFC WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       30.87        10.03         6.64        11.57         1.12         1.35 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 
        1.08         9.47         2.43        23.90        11.11         0.20 
TCGA-GN-A266 
       10.09 

VEGFC WILD-TYPE 
            0.2 
VEGFC WILD-TYPE 
          30.87 
VEGFC WILD-TYPE 
           9.47 
[1] "0.2 - 30.9 (9.5)"
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" 
     TCGA-GN-A266 
"VEGFC WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" 
     TCGA-GN-A266 
"VEGFC WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
"VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" "VEGFC WILD-TYPE" 
     TCGA-GN-A266 
"VEGFC WILD-TYPE" 
D69V2, continuous
                 vv
clus              DISTANT METASTASIS
  VEGFC MUTATED                    3
  VEGFC WILD-TYPE                  4
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  VEGFC MUTATED                                                                                          0
  VEGFC WILD-TYPE                                                                                        5
                 vv
clus              REGIONAL LYMPH NODE
  VEGFC MUTATED                     3
  VEGFC WILD-TYPE                  10
D69V3, multiclass
                                                                                          clus
vv                                                                                         VEGFC MUTATED
  DISTANT METASTASIS                                                                                   3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         VEGFC WILD-TYPE
  DISTANT METASTASIS                                                                                     4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                   10
D69V4, binary
                 cls
clus               0  1
  VEGFC MUTATED    4  2
  VEGFC WILD-TYPE  4 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEGFC MUTATED      4    2
  VEGFC WILD-TYPE    4   15
        clus
vv       VEGFC MUTATED VEGFC WILD-TYPE
  FEMALE             4               4
  MALE               2              15
                 vv
clus              N0 N1B N2C N3
  VEGFC MUTATED    4   0   1  0
  VEGFC WILD-TYPE 12   3   1  2
D69V5, multiclass
     clus
vv    VEGFC MUTATED VEGFC WILD-TYPE
  N0              4              12
  N1B             0               3
  N2C             1               1
  N3              0               2
D69V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  VEGFC MUTATED          1        0        1         2          1          0
  VEGFC WILD-TYPE        2        1        5         1          2          4
                 vv
clus              STAGE IV
  VEGFC MUTATED          0
  VEGFC WILD-TYPE        1
D69V7, multiclass

Clustering(70) Variable = TMEM202 MUTATION ANALYSIS
D70V1, survival
                   sevent
clus2               0 1
  TMEM202 MUTATED   0 3
  TMEM202 WILD-TYPE 3 7
  TMEM202 MUTATED TMEM202 WILD-TYPE 
                3                10 
  TMEM202 MUTATED TMEM202 WILD-TYPE 
                3                 7 
$`TMEM202 MUTATED`
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29V 
        1.12         1.35         2.43 

$`TMEM202 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29N 
       30.87        10.03         6.64        11.57         1.08         9.47 
TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
       23.90        11.11         0.20        10.09 

  TMEM202 MUTATED TMEM202 WILD-TYPE 
             1.12              0.20 
  TMEM202 MUTATED TMEM202 WILD-TYPE 
             2.43             30.87 
  TMEM202 MUTATED TMEM202 WILD-TYPE 
             1.35             10.06 
[1] "1.1 - 2.4 (1.4)"   "0.2 - 30.9 (10.1)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "TMEM202 MUTATED"   "TMEM202 MUTATED" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
  "TMEM202 MUTATED" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-GN-A266 
"TMEM202 WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "TMEM202 MUTATED"   "TMEM202 MUTATED" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
  "TMEM202 MUTATED" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-GN-A266 
"TMEM202 WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "TMEM202 MUTATED"   "TMEM202 MUTATED" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-ER-A19F        TCGA-FW-A3I3 
  "TMEM202 MUTATED" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" "TMEM202 WILD-TYPE" 
       TCGA-GN-A266 
"TMEM202 WILD-TYPE" 
[1] "hr=" "13" 
D70V2, continuous
                   vv
clus                DISTANT METASTASIS
  TMEM202 MUTATED                    3
  TMEM202 WILD-TYPE                  4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  TMEM202 MUTATED                                                                                          0
  TMEM202 WILD-TYPE                                                                                        5
                   vv
clus                REGIONAL LYMPH NODE
  TMEM202 MUTATED                     2
  TMEM202 WILD-TYPE                  11
D70V3, multiclass
                                                                                          clus
vv                                                                                         TMEM202 MUTATED
  DISTANT METASTASIS                                                                                     3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         TMEM202 WILD-TYPE
  DISTANT METASTASIS                                                                                       4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 5
  REGIONAL LYMPH NODE                                                                                     11
D70V4, binary
                   cls
clus                 0  1
  TMEM202 MUTATED    3  2
  TMEM202 WILD-TYPE  5 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM202 MUTATED      3    2
  TMEM202 WILD-TYPE    5   15
        clus
vv       TMEM202 MUTATED TMEM202 WILD-TYPE
  FEMALE               3                 5
  MALE                 2                15
                   vv
clus                N0 N1B N2C N3
  TMEM202 MUTATED    2   2   0  0
  TMEM202 WILD-TYPE 14   1   2  2
D70V5, multiclass
     clus
vv    TMEM202 MUTATED TMEM202 WILD-TYPE
  N0                2                14
  N1B               2                 1
  N2C               0                 2
  N3                0                 2
D70V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  TMEM202 MUTATED          0        0        2         0          0          2
  TMEM202 WILD-TYPE        3        1        4         3          3          2
                   vv
clus                STAGE IV
  TMEM202 MUTATED          0
  TMEM202 WILD-TYPE        1
D70V7, multiclass

Clustering(71) Variable = ERC2 MUTATION ANALYSIS
D71V1, survival
                sevent
clus2            0 1
  ERC2 MUTATED   2 3
  ERC2 WILD-TYPE 1 7
  ERC2 MUTATED ERC2 WILD-TYPE 
             5              8 
  ERC2 MUTATED ERC2 WILD-TYPE 
             3              7 
$`ERC2 MUTATED`
TCGA-D3-A2JF TCGA-EE-A181 TCGA-EE-A2A2 TCGA-ER-A19F TCGA-GN-A266 
       30.87         1.12        23.90        11.11        10.09 

$`ERC2 WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
       10.03         6.64        11.57         1.35         1.08         9.47 
TCGA-EE-A29V TCGA-FW-A3I3 
        2.43         0.20 

  ERC2 MUTATED ERC2 WILD-TYPE 
          1.12           0.20 
  ERC2 MUTATED ERC2 WILD-TYPE 
         30.87          11.57 
  ERC2 MUTATED ERC2 WILD-TYPE 
        11.110          4.535 
[1] "1.1 - 30.9 (11.1)" "0.2 - 11.6 (4.5)" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
  "ERC2 MUTATED" "ERC2 WILD-TYPE" "ERC2 WILD-TYPE" "ERC2 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "ERC2 MUTATED" "ERC2 WILD-TYPE" "ERC2 WILD-TYPE" "ERC2 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"ERC2 WILD-TYPE"   "ERC2 MUTATED"   "ERC2 MUTATED" "ERC2 WILD-TYPE" 
    TCGA-GN-A266 
  "ERC2 MUTATED" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
  "ERC2 MUTATED" "ERC2 WILD-TYPE" "ERC2 WILD-TYPE" "ERC2 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "ERC2 MUTATED" "ERC2 WILD-TYPE" "ERC2 WILD-TYPE" "ERC2 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"ERC2 WILD-TYPE"   "ERC2 MUTATED"   "ERC2 MUTATED" "ERC2 WILD-TYPE" 
    TCGA-GN-A266 
  "ERC2 MUTATED" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
  "ERC2 MUTATED" "ERC2 WILD-TYPE" "ERC2 WILD-TYPE" "ERC2 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "ERC2 MUTATED" "ERC2 WILD-TYPE" "ERC2 WILD-TYPE" "ERC2 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"ERC2 WILD-TYPE"   "ERC2 MUTATED"   "ERC2 MUTATED" "ERC2 WILD-TYPE" 
    TCGA-GN-A266 
  "ERC2 MUTATED" 
[1] "hr=" "3.4"
D71V2, continuous
                vv
clus             DISTANT METASTASIS
  ERC2 MUTATED                    1
  ERC2 WILD-TYPE                  6
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ERC2 MUTATED                                                                                          2
  ERC2 WILD-TYPE                                                                                        3
                vv
clus             REGIONAL LYMPH NODE
  ERC2 MUTATED                     9
  ERC2 WILD-TYPE                   4
D71V3, multiclass
                                                                                          clus
vv                                                                                         ERC2 MUTATED
  DISTANT METASTASIS                                                                                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            2
  REGIONAL LYMPH NODE                                                                                 9
                                                                                          clus
vv                                                                                         ERC2 WILD-TYPE
  DISTANT METASTASIS                                                                                    6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              3
  REGIONAL LYMPH NODE                                                                                   4
D71V4, binary
                cls
clus              0  1
  ERC2 MUTATED    1 11
  ERC2 WILD-TYPE  7  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERC2 MUTATED      1   11
  ERC2 WILD-TYPE    7    6
        clus
vv       ERC2 MUTATED ERC2 WILD-TYPE
  FEMALE            1              7
  MALE             11              6
                vv
clus             N0 N1B N2C N3
  ERC2 MUTATED   10   1   0  0
  ERC2 WILD-TYPE  6   2   2  2
D71V5, multiclass
     clus
vv    ERC2 MUTATED ERC2 WILD-TYPE
  N0            10              6
  N1B            1              2
  N2C            0              2
  N3             0              2
D71V6, continuous
                vv
clus             STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  ERC2 MUTATED          1        1        5         2          1          0
  ERC2 WILD-TYPE        2        0        1         1          2          4
                vv
clus             STAGE IV
  ERC2 MUTATED          0
  ERC2 WILD-TYPE        1
D71V7, multiclass

Clustering(72) Variable = GRM3 MUTATION ANALYSIS
D72V1, survival
                sevent
clus2            0 1
  GRM3 MUTATED   1 3
  GRM3 WILD-TYPE 2 7
  GRM3 MUTATED GRM3 WILD-TYPE 
             4              9 
  GRM3 MUTATED GRM3 WILD-TYPE 
             3              7 
$`GRM3 MUTATED`
TCGA-D3-A2JF TCGA-EE-A181 TCGA-ER-A19F TCGA-GN-A266 
       30.87         1.12        11.11        10.09 

$`GRM3 WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
       10.03         6.64        11.57         1.35         1.08         9.47 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-FW-A3I3 
        2.43        23.90         0.20 

  GRM3 MUTATED GRM3 WILD-TYPE 
          1.12           0.20 
  GRM3 MUTATED GRM3 WILD-TYPE 
         30.87          23.90 
  GRM3 MUTATED GRM3 WILD-TYPE 
         10.60           6.64 
[1] "1.1 - 30.9 (10.6)" "0.2 - 23.9 (6.6)" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
  "GRM3 MUTATED" "GRM3 WILD-TYPE" "GRM3 WILD-TYPE" "GRM3 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "GRM3 MUTATED" "GRM3 WILD-TYPE" "GRM3 WILD-TYPE" "GRM3 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"GRM3 WILD-TYPE" "GRM3 WILD-TYPE"   "GRM3 MUTATED" "GRM3 WILD-TYPE" 
    TCGA-GN-A266 
  "GRM3 MUTATED" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
  "GRM3 MUTATED" "GRM3 WILD-TYPE" "GRM3 WILD-TYPE" "GRM3 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "GRM3 MUTATED" "GRM3 WILD-TYPE" "GRM3 WILD-TYPE" "GRM3 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"GRM3 WILD-TYPE" "GRM3 WILD-TYPE"   "GRM3 MUTATED" "GRM3 WILD-TYPE" 
    TCGA-GN-A266 
  "GRM3 MUTATED" 
    TCGA-D3-A2JF     TCGA-DA-A1I0     TCGA-DA-A1IC     TCGA-EE-A17X 
  "GRM3 MUTATED" "GRM3 WILD-TYPE" "GRM3 WILD-TYPE" "GRM3 WILD-TYPE" 
    TCGA-EE-A181     TCGA-EE-A182     TCGA-EE-A29L     TCGA-EE-A29N 
  "GRM3 MUTATED" "GRM3 WILD-TYPE" "GRM3 WILD-TYPE" "GRM3 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A2A2     TCGA-ER-A19F     TCGA-FW-A3I3 
"GRM3 WILD-TYPE" "GRM3 WILD-TYPE"   "GRM3 MUTATED" "GRM3 WILD-TYPE" 
    TCGA-GN-A266 
  "GRM3 MUTATED" 
[1] "hr=" "1.6"
D72V2, continuous
                vv
clus             DISTANT METASTASIS
  GRM3 MUTATED                    2
  GRM3 WILD-TYPE                  5
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  GRM3 MUTATED                                                                                          2
  GRM3 WILD-TYPE                                                                                        3
                vv
clus             REGIONAL LYMPH NODE
  GRM3 MUTATED                     6
  GRM3 WILD-TYPE                   7
D72V3, multiclass
                                                                                          clus
vv                                                                                         GRM3 MUTATED
  DISTANT METASTASIS                                                                                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            2
  REGIONAL LYMPH NODE                                                                                 6
                                                                                          clus
vv                                                                                         GRM3 WILD-TYPE
  DISTANT METASTASIS                                                                                    5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              3
  REGIONAL LYMPH NODE                                                                                   7
D72V4, binary
                cls
clus             0 1
  GRM3 MUTATED   2 8
  GRM3 WILD-TYPE 6 9
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM3 MUTATED      2    8
  GRM3 WILD-TYPE    6    9
        clus
vv       GRM3 MUTATED GRM3 WILD-TYPE
  FEMALE            2              6
  MALE              8              9
                vv
clus             N0 N1B N2C N3
  GRM3 MUTATED    9   0   0  0
  GRM3 WILD-TYPE  7   3   2  2
D72V5, multiclass
     clus
vv    GRM3 MUTATED GRM3 WILD-TYPE
  N0             9              7
  N1B            0              3
  N2C            0              2
  N3             0              2
D72V6, continuous
                vv
clus             STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  GRM3 MUTATED          1        1        4         2          0          0
  GRM3 WILD-TYPE        2        0        2         1          3          4
                vv
clus             STAGE IV
  GRM3 MUTATED          0
  GRM3 WILD-TYPE        1
D72V7, multiclass

Clustering(73) Variable = CDH12 MUTATION ANALYSIS
D73V1, survival
                 sevent
clus2              0  1
  CDH12 MUTATED    1  0
  CDH12 WILD-TYPE  2 10
  CDH12 MUTATED CDH12 WILD-TYPE 
              1              12 
  CDH12 MUTATED CDH12 WILD-TYPE 
              0              10 
$`CDH12 MUTATED`
TCGA-D3-A2JF 
       30.87 

$`CDH12 WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L 
       10.03         6.64        11.57         1.12         1.35         1.08 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        9.47         2.43        23.90        11.11         0.20        10.09 

  CDH12 MUTATED CDH12 WILD-TYPE 
          30.87            0.20 
  CDH12 MUTATED CDH12 WILD-TYPE 
          30.87           23.90 
  CDH12 MUTATED CDH12 WILD-TYPE 
         30.870           8.055 
[1] "30.9 - 30.9 (30.9)" "0.2 - 23.9 (8.1)"  
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "CDH12 MUTATED" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" 
     TCGA-GN-A266 
"CDH12 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "CDH12 MUTATED" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" 
     TCGA-GN-A266 
"CDH12 WILD-TYPE" 
     TCGA-D3-A2JF      TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X 
  "CDH12 MUTATED" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" 
     TCGA-EE-A181      TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N 
"CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3 
"CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" 
     TCGA-GN-A266 
"CDH12 WILD-TYPE" 
[1] "Remove cluster labels:" "CDH12 MUTATED"         
clus
  CDH12 MUTATED CDH12 WILD-TYPE 
              1              12 
     TCGA-DA-A1I0      TCGA-DA-A1IC      TCGA-EE-A17X      TCGA-EE-A181 
"CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" 
     TCGA-EE-A182      TCGA-EE-A29L      TCGA-EE-A29N      TCGA-EE-A29V 
"CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-ER-A19F      TCGA-FW-A3I3      TCGA-GN-A266 
"CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" "CDH12 WILD-TYPE" 
D73V2, continuous
                 vv
clus              DISTANT METASTASIS
  CDH12 MUTATED                    4
  CDH12 WILD-TYPE                  3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CDH12 MUTATED                                                                                          1
  CDH12 WILD-TYPE                                                                                        4
                 vv
clus              REGIONAL LYMPH NODE
  CDH12 MUTATED                     3
  CDH12 WILD-TYPE                  10
D73V3, multiclass
                                                                                          clus
vv                                                                                         CDH12 MUTATED
  DISTANT METASTASIS                                                                                   4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         CDH12 WILD-TYPE
  DISTANT METASTASIS                                                                                     3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                   10
D73V4, binary
                 cls
clus               0  1
  CDH12 MUTATED    4  4
  CDH12 WILD-TYPE  4 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH12 MUTATED      4    4
  CDH12 WILD-TYPE    4   13
        clus
vv       CDH12 MUTATED CDH12 WILD-TYPE
  FEMALE             4               4
  MALE               4              13
                 vv
clus              N0 N1B N2C N3
  CDH12 MUTATED    6   0   1  0
  CDH12 WILD-TYPE 10   3   1  2
D73V5, multiclass
     clus
vv    CDH12 MUTATED CDH12 WILD-TYPE
  N0              6              10
  N1B             0               3
  N2C             1               1
  N3              0               2
D73V6, continuous
                 vv
clus              STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  CDH12 MUTATED          2        0        1         3          1          0
  CDH12 WILD-TYPE        1        1        5         0          2          4
                 vv
clus              STAGE IV
  CDH12 MUTATED          0
  CDH12 WILD-TYPE        1
D73V7, multiclass

Clustering(74) Variable = SIRPB1 MUTATION ANALYSIS
D74V1, survival
                  sevent
clus2              0 1
  SIRPB1 MUTATED   0 3
  SIRPB1 WILD-TYPE 3 7
  SIRPB1 MUTATED SIRPB1 WILD-TYPE 
               3               10 
  SIRPB1 MUTATED SIRPB1 WILD-TYPE 
               3                7 
$`SIRPB1 MUTATED`
TCGA-EE-A29L TCGA-ER-A19F TCGA-GN-A266 
        1.08        11.11        10.09 

$`SIRPB1 WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       30.87        10.03         6.64        11.57         1.12         1.35 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-FW-A3I3 
        9.47         2.43        23.90         0.20 

  SIRPB1 MUTATED SIRPB1 WILD-TYPE 
            1.08             0.20 
  SIRPB1 MUTATED SIRPB1 WILD-TYPE 
           11.11            30.87 
  SIRPB1 MUTATED SIRPB1 WILD-TYPE 
          10.090            8.055 
[1] "1.1 - 11.1 (10.1)" "0.2 - 30.9 (8.1)" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE"   "SIRPB1 MUTATED" "SIRPB1 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE"   "SIRPB1 MUTATED" "SIRPB1 WILD-TYPE" 
      TCGA-GN-A266 
  "SIRPB1 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE"   "SIRPB1 MUTATED" "SIRPB1 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE"   "SIRPB1 MUTATED" "SIRPB1 WILD-TYPE" 
      TCGA-GN-A266 
  "SIRPB1 MUTATED" 
      TCGA-D3-A2JF       TCGA-DA-A1I0       TCGA-DA-A1IC       TCGA-EE-A17X 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" 
      TCGA-EE-A181       TCGA-EE-A182       TCGA-EE-A29L       TCGA-EE-A29N 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE"   "SIRPB1 MUTATED" "SIRPB1 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A2A2       TCGA-ER-A19F       TCGA-FW-A3I3 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE"   "SIRPB1 MUTATED" "SIRPB1 WILD-TYPE" 
      TCGA-GN-A266 
  "SIRPB1 MUTATED" 
[1] "hr=" "1.4"
D74V2, continuous
                  vv
clus               DISTANT METASTASIS
  SIRPB1 MUTATED                    0
  SIRPB1 WILD-TYPE                  7
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  SIRPB1 MUTATED                                                                                          1
  SIRPB1 WILD-TYPE                                                                                        4
                  vv
clus               REGIONAL LYMPH NODE
  SIRPB1 MUTATED                     5
  SIRPB1 WILD-TYPE                   8
D74V3, multiclass
                                                                                          clus
vv                                                                                         SIRPB1 MUTATED
  DISTANT METASTASIS                                                                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   5
                                                                                          clus
vv                                                                                         SIRPB1 WILD-TYPE
  DISTANT METASTASIS                                                                                      7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                     8
D74V4, binary
                  cls
clus                0  1
  SIRPB1 MUTATED    0  6
  SIRPB1 WILD-TYPE  8 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SIRPB1 MUTATED      0    6
  SIRPB1 WILD-TYPE    8   11
        clus
vv       SIRPB1 MUTATED SIRPB1 WILD-TYPE
  FEMALE              0                8
  MALE                6               11
                  vv
clus               N0 N1B N2C N3
  SIRPB1 MUTATED    4   0   0  1
  SIRPB1 WILD-TYPE 12   3   2  1
D74V5, multiclass
     clus
vv    SIRPB1 MUTATED SIRPB1 WILD-TYPE
  N0               4               12
  N1B              0                3
  N2C              0                2
  N3               1                1
D74V6, continuous
                  vv
clus               STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  SIRPB1 MUTATED          0        0        2         1          0          1
  SIRPB1 WILD-TYPE        3        1        4         2          3          3
                  vv
clus               STAGE IV
  SIRPB1 MUTATED          0
  SIRPB1 WILD-TYPE        1
D74V7, multiclass
                     V1.D                        V2                        V3 
          "Time to Death"                     "AGE" "PRIMARY.SITE.OF.DISEASE" 
                       V4                        V5                        V6 
                 "GENDER"   "LYMPH.NODE.METASTASIS"         "TUMOR.STAGECODE" 
                       V7 
  "NEOPLASM.DISEASESTAGE" 
> q(save="no")
