
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/404231/SKCM-NRAS_Hotspot_Mutants.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-NRAS_Hotspot_Mutants/3215657/SKCM-NRAS_Hotspot_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=45, in cluster file=62, common to both=45
[1] "Reduce the number of clustering variables from 108 to 99."
[1] 99 45
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              11               34 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              11               34 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             9             36 
  TP53 MUTATED TP53 WILD-TYPE 
             9             36 
[1] "MUM1L1 MUTATION ANALYSIS"
[1] 3
  MUM1L1 MUTATED MUM1L1 WILD-TYPE 
               7               38 
  MUM1L1 MUTATED MUM1L1 WILD-TYPE 
               7               38 
[1] "CD163L1 MUTATION ANALYSIS"
[1] 3
  CD163L1 MUTATED CD163L1 WILD-TYPE 
               13                32 
  CD163L1 MUTATED CD163L1 WILD-TYPE 
               13                32 
[1] "PSG4 MUTATION ANALYSIS"
[1] 3
  PSG4 MUTATED PSG4 WILD-TYPE 
             8             37 
  PSG4 MUTATED PSG4 WILD-TYPE 
             8             37 
[1] "PPP6C MUTATION ANALYSIS"
[1] 3
  PPP6C MUTATED PPP6C WILD-TYPE 
              9              36 
  PPP6C MUTATED PPP6C WILD-TYPE 
              9              36 
[1] "ZNF99 MUTATION ANALYSIS"
[1] 3
  ZNF99 MUTATED ZNF99 WILD-TYPE 
             13              32 
  ZNF99 MUTATED ZNF99 WILD-TYPE 
             13              32 
[1] "KHDRBS2 MUTATION ANALYSIS"
[1] 3
  KHDRBS2 MUTATED KHDRBS2 WILD-TYPE 
                8                37 
  KHDRBS2 MUTATED KHDRBS2 WILD-TYPE 
                8                37 
[1] "POTEG MUTATION ANALYSIS"
[1] 3
  POTEG MUTATED POTEG WILD-TYPE 
              8              37 
  POTEG MUTATED POTEG WILD-TYPE 
              8              37 
[1] "MARCO MUTATION ANALYSIS"
[1] 3
  MARCO MUTATED MARCO WILD-TYPE 
              9              36 
  MARCO MUTATED MARCO WILD-TYPE 
              9              36 
[1] "SGCZ MUTATION ANALYSIS"
[1] 3
  SGCZ MUTATED SGCZ WILD-TYPE 
             8             37 
  SGCZ MUTATED SGCZ WILD-TYPE 
             8             37 
[1] "GLRB MUTATION ANALYSIS"
[1] 3
  GLRB MUTATED GLRB WILD-TYPE 
             9             36 
  GLRB MUTATED GLRB WILD-TYPE 
             9             36 
[1] "OR2W1 MUTATION ANALYSIS"
[1] 3
  OR2W1 MUTATED OR2W1 WILD-TYPE 
              6              39 
  OR2W1 MUTATED OR2W1 WILD-TYPE 
              6              39 
[1] "C4ORF22 MUTATION ANALYSIS"
[1] 3
  C4ORF22 MUTATED C4ORF22 WILD-TYPE 
                5                40 
  C4ORF22 MUTATED C4ORF22 WILD-TYPE 
                5                40 
[1] "UGT2B28 MUTATION ANALYSIS"
[1] 3
  UGT2B28 MUTATED UGT2B28 WILD-TYPE 
                8                37 
  UGT2B28 MUTATED UGT2B28 WILD-TYPE 
                8                37 
[1] "ZNF676 MUTATION ANALYSIS"
[1] 3
  ZNF676 MUTATED ZNF676 WILD-TYPE 
              10               35 
  ZNF676 MUTATED ZNF676 WILD-TYPE 
              10               35 
[1] "LIPI MUTATION ANALYSIS"
[1] 3
  LIPI MUTATED LIPI WILD-TYPE 
             7             38 
  LIPI MUTATED LIPI WILD-TYPE 
             7             38 
[1] "CADM2 MUTATION ANALYSIS"
[1] 3
  CADM2 MUTATED CADM2 WILD-TYPE 
              5              40 
  CADM2 MUTATED CADM2 WILD-TYPE 
              5              40 
[1] "CDH9 MUTATION ANALYSIS"
[1] 3
  CDH9 MUTATED CDH9 WILD-TYPE 
             9             36 
  CDH9 MUTATED CDH9 WILD-TYPE 
             9             36 
[1] "OR52E2 MUTATION ANALYSIS"
[1] 3
  OR52E2 MUTATED OR52E2 WILD-TYPE 
               6               39 
  OR52E2 MUTATED OR52E2 WILD-TYPE 
               6               39 
[1] "CLEC5A MUTATION ANALYSIS"
[1] 3
  CLEC5A MUTATED CLEC5A WILD-TYPE 
               4               41 
  CLEC5A MUTATED CLEC5A WILD-TYPE 
               4               41 
[1] "HIST1H2AA MUTATION ANALYSIS"
[1] 3
  HIST1H2AA MUTATED HIST1H2AA WILD-TYPE 
                  3                  42 
  HIST1H2AA MUTATED HIST1H2AA WILD-TYPE 
                  3                  42 
[1] "KIAA1257 MUTATION ANALYSIS"
[1] 3
  KIAA1257 MUTATED KIAA1257 WILD-TYPE 
                 4                 41 
  KIAA1257 MUTATED KIAA1257 WILD-TYPE 
                 4                 41 
[1] "PCDH18 MUTATION ANALYSIS"
[1] 3
  PCDH18 MUTATED PCDH18 WILD-TYPE 
               9               36 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
               9               36 
[1] "SPOCK3 MUTATION ANALYSIS"
[1] 3
  SPOCK3 MUTATED SPOCK3 WILD-TYPE 
               6               39 
  SPOCK3 MUTATED SPOCK3 WILD-TYPE 
               6               39 
[1] "OR2G6 MUTATION ANALYSIS"
[1] 3
  OR2G6 MUTATED OR2G6 WILD-TYPE 
              8              37 
  OR2G6 MUTATED OR2G6 WILD-TYPE 
              8              37 
[1] "STXBP5L MUTATION ANALYSIS"
[1] 3
  STXBP5L MUTATED STXBP5L WILD-TYPE 
               10                35 
  STXBP5L MUTATED STXBP5L WILD-TYPE 
               10                35 
[1] "CNGB3 MUTATION ANALYSIS"
[1] 3
  CNGB3 MUTATED CNGB3 WILD-TYPE 
              9              36 
  CNGB3 MUTATED CNGB3 WILD-TYPE 
              9              36 
[1] "HHIPL2 MUTATION ANALYSIS"
[1] 3
  HHIPL2 MUTATED HHIPL2 WILD-TYPE 
               3               42 
  HHIPL2 MUTATED HHIPL2 WILD-TYPE 
               3               42 
[1] "OR10G8 MUTATION ANALYSIS"
[1] 3
  OR10G8 MUTATED OR10G8 WILD-TYPE 
               4               41 
  OR10G8 MUTATED OR10G8 WILD-TYPE 
               4               41 
[1] "UGT2B4 MUTATION ANALYSIS"
[1] 3
  UGT2B4 MUTATED UGT2B4 WILD-TYPE 
               8               37 
  UGT2B4 MUTATED UGT2B4 WILD-TYPE 
               8               37 
[1] "ZBBX MUTATION ANALYSIS"
[1] 3
  ZBBX MUTATED ZBBX WILD-TYPE 
             9             36 
  ZBBX MUTATED ZBBX WILD-TYPE 
             9             36 
[1] "C1QTNF9 MUTATION ANALYSIS"
[1] 3
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
                3                42 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
                3                42 
[1] "HCRTR2 MUTATION ANALYSIS"
[1] 3
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               7               38 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               7               38 
[1] "KRT78 MUTATION ANALYSIS"
[1] 3
  KRT78 MUTATED KRT78 WILD-TYPE 
              5              40 
  KRT78 MUTATED KRT78 WILD-TYPE 
              5              40 
[1] "BCLAF1 MUTATION ANALYSIS"
[1] 3
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               9               36 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               9               36 
[1] "LPAR1 MUTATION ANALYSIS"
[1] 3
  LPAR1 MUTATED LPAR1 WILD-TYPE 
              3              42 
  LPAR1 MUTATED LPAR1 WILD-TYPE 
              3              42 
[1] "STK31 MUTATION ANALYSIS"
[1] 3
  STK31 MUTATED STK31 WILD-TYPE 
              6              39 
  STK31 MUTATED STK31 WILD-TYPE 
              6              39 
[1] "HBG2 MUTATION ANALYSIS"
[1] 3
  HBG2 MUTATED HBG2 WILD-TYPE 
             4             41 
  HBG2 MUTATED HBG2 WILD-TYPE 
             4             41 
[1] "BAGE2 MUTATION ANALYSIS"
[1] 3
  BAGE2 MUTATED BAGE2 WILD-TYPE 
              3              42 
  BAGE2 MUTATED BAGE2 WILD-TYPE 
              3              42 
[1] "ADH1B MUTATION ANALYSIS"
[1] 3
  ADH1B MUTATED ADH1B WILD-TYPE 
              6              39 
  ADH1B MUTATED ADH1B WILD-TYPE 
              6              39 
[1] "CNTN4 MUTATION ANALYSIS"
[1] 3
  CNTN4 MUTATED CNTN4 WILD-TYPE 
             10              35 
  CNTN4 MUTATED CNTN4 WILD-TYPE 
             10              35 
[1] "DEFA4 MUTATION ANALYSIS"
[1] 3
  DEFA4 MUTATED DEFA4 WILD-TYPE 
              4              41 
  DEFA4 MUTATED DEFA4 WILD-TYPE 
              4              41 
[1] "GFRAL MUTATION ANALYSIS"
[1] 3
  GFRAL MUTATED GFRAL WILD-TYPE 
              8              37 
  GFRAL MUTATED GFRAL WILD-TYPE 
              8              37 
[1] "ST8SIA3 MUTATION ANALYSIS"
[1] 3
  ST8SIA3 MUTATED ST8SIA3 WILD-TYPE 
                6                39 
  ST8SIA3 MUTATED ST8SIA3 WILD-TYPE 
                6                39 
[1] "DSPP MUTATION ANALYSIS"
[1] 3
  DSPP MUTATED DSPP WILD-TYPE 
             5             40 
  DSPP MUTATED DSPP WILD-TYPE 
             5             40 
[1] "OR10K2 MUTATION ANALYSIS"
[1] 3
  OR10K2 MUTATED OR10K2 WILD-TYPE 
               7               38 
  OR10K2 MUTATED OR10K2 WILD-TYPE 
               7               38 
[1] "CLEC17A MUTATION ANALYSIS"
[1] 3
  CLEC17A MUTATED CLEC17A WILD-TYPE 
                3                42 
  CLEC17A MUTATED CLEC17A WILD-TYPE 
                3                42 
[1] "POU6F2 MUTATION ANALYSIS"
[1] 3
  POU6F2 MUTATED POU6F2 WILD-TYPE 
               8               37 
  POU6F2 MUTATED POU6F2 WILD-TYPE 
               8               37 
[1] "LRRIQ3 MUTATION ANALYSIS"
[1] 3
  LRRIQ3 MUTATED LRRIQ3 WILD-TYPE 
               7               38 
  LRRIQ3 MUTATED LRRIQ3 WILD-TYPE 
               7               38 
[1] "ARID2 MUTATION ANALYSIS"
[1] 3
  ARID2 MUTATED ARID2 WILD-TYPE 
              9              36 
  ARID2 MUTATED ARID2 WILD-TYPE 
              9              36 
[1] "GAS2 MUTATION ANALYSIS"
[1] 3
  GAS2 MUTATED GAS2 WILD-TYPE 
             5             40 
  GAS2 MUTATED GAS2 WILD-TYPE 
             5             40 
[1] "SIRPB1 MUTATION ANALYSIS"
[1] 3
  SIRPB1 MUTATED SIRPB1 WILD-TYPE 
               6               39 
  SIRPB1 MUTATED SIRPB1 WILD-TYPE 
               6               39 
[1] "ACTC1 MUTATION ANALYSIS"
[1] 3
  ACTC1 MUTATED ACTC1 WILD-TYPE 
              4              41 
  ACTC1 MUTATED ACTC1 WILD-TYPE 
              4              41 
[1] "PRB2 MUTATION ANALYSIS"
[1] 3
  PRB2 MUTATED PRB2 WILD-TYPE 
             5             40 
  PRB2 MUTATED PRB2 WILD-TYPE 
             5             40 
[1] "C15ORF23 MUTATION ANALYSIS"
[1] 3
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                 3                 42 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                 3                 42 
[1] "FASLG MUTATION ANALYSIS"
[1] 3
  FASLG MUTATED FASLG WILD-TYPE 
              3              42 
  FASLG MUTATED FASLG WILD-TYPE 
              3              42 
[1] "PAK7 MUTATION ANALYSIS"
[1] 3
  PAK7 MUTATED PAK7 WILD-TYPE 
             9             36 
  PAK7 MUTATED PAK7 WILD-TYPE 
             9             36 
[1] "SIGLEC14 MUTATION ANALYSIS"
[1] 3
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 3                 42 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 3                 42 
[1] "TPTE2 MUTATION ANALYSIS"
[1] 3
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              6              39 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              6              39 
[1] "APBB1IP MUTATION ANALYSIS"
[1] 3
  APBB1IP MUTATED APBB1IP WILD-TYPE 
                5                40 
  APBB1IP MUTATED APBB1IP WILD-TYPE 
                5                40 
[1] "ANGPT1 MUTATION ANALYSIS"
[1] 3
  ANGPT1 MUTATED ANGPT1 WILD-TYPE 
               6               39 
  ANGPT1 MUTATED ANGPT1 WILD-TYPE 
               6               39 
[1] "ARMC4 MUTATION ANALYSIS"
[1] 3
  ARMC4 MUTATED ARMC4 WILD-TYPE 
             11              34 
  ARMC4 MUTATED ARMC4 WILD-TYPE 
             11              34 
[1] "CYP4X1 MUTATION ANALYSIS"
[1] 3
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               4               41 
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               4               41 
[1] "DSG1 MUTATION ANALYSIS"
[1] 3
  DSG1 MUTATED DSG1 WILD-TYPE 
             6             39 
  DSG1 MUTATED DSG1 WILD-TYPE 
             6             39 
[1] "ADAM7 MUTATION ANALYSIS"
[1] 3
  ADAM7 MUTATED ADAM7 WILD-TYPE 
             10              35 
  ADAM7 MUTATED ADAM7 WILD-TYPE 
             10              35 
[1] "KCNQ5 MUTATION ANALYSIS"
[1] 3
  KCNQ5 MUTATED KCNQ5 WILD-TYPE 
              8              37 
  KCNQ5 MUTATED KCNQ5 WILD-TYPE 
              8              37 
[1] "POF1B MUTATION ANALYSIS"
[1] 3
  POF1B MUTATED POF1B WILD-TYPE 
              8              37 
  POF1B MUTATED POF1B WILD-TYPE 
              8              37 
[1] "TCEB3C MUTATION ANALYSIS"
[1] 3
  TCEB3C MUTATED TCEB3C WILD-TYPE 
               6               39 
  TCEB3C MUTATED TCEB3C WILD-TYPE 
               6               39 
[1] "F2RL1 MUTATION ANALYSIS"
[1] 3
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              5              40 
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              5              40 
[1] "SNCAIP MUTATION ANALYSIS"
[1] 3
  SNCAIP MUTATED SNCAIP WILD-TYPE 
               9               36 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
               9               36 
[1] "LOC649330 MUTATION ANALYSIS"
[1] 3
  LOC649330 MUTATED LOC649330 WILD-TYPE 
                  7                  38 
  LOC649330 MUTATED LOC649330 WILD-TYPE 
                  7                  38 
[1] "UGT2A3 MUTATION ANALYSIS"
[1] 3
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
               6               39 
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
               6               39 
[1] "NDUFA13 MUTATION ANALYSIS"
[1] 3
  NDUFA13 MUTATED NDUFA13 WILD-TYPE 
                4                41 
  NDUFA13 MUTATED NDUFA13 WILD-TYPE 
                4                41 
[1] "ZIM3 MUTATION ANALYSIS"
[1] 3
  ZIM3 MUTATED ZIM3 WILD-TYPE 
             4             41 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
             4             41 
[1] "DDX3X MUTATION ANALYSIS"
[1] 3
  DDX3X MUTATED DDX3X WILD-TYPE 
              6              39 
  DDX3X MUTATED DDX3X WILD-TYPE 
              6              39 
[1] "LILRB4 MUTATION ANALYSIS"
[1] 3
  LILRB4 MUTATED LILRB4 WILD-TYPE 
               6               39 
  LILRB4 MUTATED LILRB4 WILD-TYPE 
               6               39 
[1] "TLR4 MUTATION ANALYSIS"
[1] 3
  TLR4 MUTATED TLR4 WILD-TYPE 
             9             36 
  TLR4 MUTATED TLR4 WILD-TYPE 
             9             36 
[1] "ZNF479 MUTATION ANALYSIS"
[1] 3
  ZNF479 MUTATED ZNF479 WILD-TYPE 
               3               42 
  ZNF479 MUTATED ZNF479 WILD-TYPE 
               3               42 
[1] "GABRG1 MUTATION ANALYSIS"
[1] 3
  GABRG1 MUTATED GABRG1 WILD-TYPE 
               3               42 
  GABRG1 MUTATED GABRG1 WILD-TYPE 
               3               42 
[1] "OR1N2 MUTATION ANALYSIS"
[1] 3
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              6              39 
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              6              39 
[1] "HHLA2 MUTATION ANALYSIS"
[1] 3
  HHLA2 MUTATED HHLA2 WILD-TYPE 
              4              41 
  HHLA2 MUTATED HHLA2 WILD-TYPE 
              4              41 
[1] "SYCE1 MUTATION ANALYSIS"
[1] 3
  SYCE1 MUTATED SYCE1 WILD-TYPE 
              4              41 
  SYCE1 MUTATED SYCE1 WILD-TYPE 
              4              41 
[1] "RGPD3 MUTATION ANALYSIS"
[1] 3
  RGPD3 MUTATED RGPD3 WILD-TYPE 
              9              36 
  RGPD3 MUTATED RGPD3 WILD-TYPE 
              9              36 
[1] "CDH10 MUTATION ANALYSIS"
[1] 3
  CDH10 MUTATED CDH10 WILD-TYPE 
             10              35 
  CDH10 MUTATED CDH10 WILD-TYPE 
             10              35 
[1] "C6ORF105 MUTATION ANALYSIS"
[1] 3
  C6ORF105 MUTATED C6ORF105 WILD-TYPE 
                 4                 41 
  C6ORF105 MUTATED C6ORF105 WILD-TYPE 
                 4                 41 
[1] "FPR2 MUTATION ANALYSIS"
[1] 3
  FPR2 MUTATED FPR2 WILD-TYPE 
             4             41 
  FPR2 MUTATED FPR2 WILD-TYPE 
             4             41 
[1] "UGT1A7 MUTATION ANALYSIS"
[1] 3
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               3               42 
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               3               42 
[1] "JAKMIP1 MUTATION ANALYSIS"
[1] 3
  JAKMIP1 MUTATED JAKMIP1 WILD-TYPE 
                5                40 
  JAKMIP1 MUTATED JAKMIP1 WILD-TYPE 
                5                40 
[1] "CYLC2 MUTATION ANALYSIS"
[1] 3
  CYLC2 MUTATED CYLC2 WILD-TYPE 
              5              40 
  CYLC2 MUTATED CYLC2 WILD-TYPE 
              5              40 
[1] "DRGX MUTATION ANALYSIS"
[1] 3
  DRGX MUTATED DRGX WILD-TYPE 
             6             39 
  DRGX MUTATED DRGX WILD-TYPE 
             6             39 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
             3             42 
  IDH1 MUTATED IDH1 WILD-TYPE 
             3             42 
[1] "ASB5 MUTATION ANALYSIS"
[1] 3
  ASB5 MUTATED ASB5 WILD-TYPE 
             3             42 
  ASB5 MUTATED ASB5 WILD-TYPE 
             3             42 
[1] "COL21A1 MUTATION ANALYSIS"
[1] 3
  COL21A1 MUTATED COL21A1 WILD-TYPE 
                9                36 
  COL21A1 MUTATED COL21A1 WILD-TYPE 
                9                36 
[1] "OR4M2 MUTATION ANALYSIS"
[1] 3
  OR4M2 MUTATED OR4M2 WILD-TYPE 
              6              39 
  OR4M2 MUTATED OR4M2 WILD-TYPE 
              6              39 
[1] "ANKRD45 MUTATION ANALYSIS"
[1] 3
  ANKRD45 MUTATED ANKRD45 WILD-TYPE 
                7                38 
  ANKRD45 MUTATED ANKRD45 WILD-TYPE 
                7                38 
[1] "LCE1B MUTATION ANALYSIS"
[1] 3
  LCE1B MUTATED LCE1B WILD-TYPE 
              4              41 
  LCE1B MUTATED LCE1B WILD-TYPE 
              4              41 
[1] "MGAM MUTATION ANALYSIS"
[1] 3
  MGAM MUTATED MGAM WILD-TYPE 
            18             27 
  MGAM MUTATED MGAM WILD-TYPE 
            18             27 
[1] "ACSM2B MUTATION ANALYSIS"
[1] 3
  ACSM2B MUTATED ACSM2B WILD-TYPE 
               6               39 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
               6               39 
[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 45 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
          NA           NA           NA          164         1484         1192 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
          NA           NA           NA           NA          247          269 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
         304           NA           NA          769          727           NA 
TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GU TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AC TCGA-ER-A19D TCGA-ER-A19N TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 
          NA           NA         1303           NA           NA           NA 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZY TCGA-GN-A267 TCGA-GN-A268 
          NA           NA           NA 
Variable 1:'AGE':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=21,	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=18,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	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
 T0 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 T4A T4B  TX 
  4   4   2   4   5   3   1   5   4   1   2   6   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 45 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=28, 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=6, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CDKN2A MUTATION ANALYSIS
D1V1, survival
                  sevent
clus2               0  1
  CDKN2A MUTATED    2  3
  CDKN2A WILD-TYPE  7 10
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               5               17 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               3               10 
$`CDKN2A MUTATED`
TCGA-D3-A3MV TCGA-DA-A1HV TCGA-EE-A185 TCGA-EE-A29V TCGA-ER-A19D 
        5.39        48.79         4.27         2.43         3.52 

$`CDKN2A WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       16.47        28.08         8.38        39.19         7.00        11.57 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A1 
        1.08         8.12         8.84         9.99         8.09        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       23.90         9.67        42.84        16.21        15.39 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            2.43             1.08 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           48.79            42.84 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
            4.27            11.57 
[1] "2.4 - 48.8 (4.3)"  "1.1 - 42.8 (11.6)"
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE"   "CDKN2A MUTATED" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
  "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"CDKN2A WILD-TYPE"   "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE"   "CDKN2A MUTATED" "CDKN2A WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE"   "CDKN2A MUTATED" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
  "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"CDKN2A WILD-TYPE"   "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE"   "CDKN2A MUTATED" "CDKN2A WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE"   "CDKN2A MUTATED" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
  "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"CDKN2A WILD-TYPE"   "CDKN2A MUTATED" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE"   "CDKN2A MUTATED" "CDKN2A WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
[1] "hr=" "1.9"
D1V2, continuous
                  vv
clus               DISTANT METASTASIS
  CDKN2A MUTATED                    2
  CDKN2A WILD-TYPE                  6
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CDKN2A MUTATED                                                                                          4
  CDKN2A WILD-TYPE                                                                                        5
                  vv
clus               REGIONAL LYMPH NODE
  CDKN2A MUTATED                     5
  CDKN2A WILD-TYPE                  23
D1V3, multiclass
                                                                                          clus
vv                                                                                         CDKN2A MUTATED
  DISTANT METASTASIS                                                                                    2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              4
  REGIONAL LYMPH NODE                                                                                   5
                                                                                          clus
vv                                                                                         CDKN2A WILD-TYPE
  DISTANT METASTASIS                                                                                      6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    23
D1V4, binary
                  cls
clus                0  1
  CDKN2A MUTATED    5  6
  CDKN2A WILD-TYPE 11 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      5    6
  CDKN2A WILD-TYPE   11   23
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              5               11
  MALE                6               23
                  vv
clus               N0 N1A N1B N2A N2B N3
  CDKN2A MUTATED    5   2   1   1   1  1
  CDKN2A WILD-TYPE 22   1   3   0   1  4
D1V5, multiclass
D1V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CDKN2A MUTATED             1       0        0        2        1         0
  CDKN2A WILD-TYPE           0       3        4        4        3         3
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CDKN2A MUTATED           0         1         0          0          4
  CDKN2A WILD-TYPE         4         1         1          1          2
                  vv
clus               STAGE IIIC STAGE IV
  CDKN2A MUTATED            2        0
  CDKN2A WILD-TYPE          4        1
D1V7, multiclass

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  TP53 MUTATED    2  3
  TP53 WILD-TYPE  7 10
  TP53 MUTATED TP53 WILD-TYPE 
             5             17 
  TP53 MUTATED TP53 WILD-TYPE 
             3             10 
$`TP53 MUTATED`
TCGA-DA-A1HV TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 
       48.79         1.08         2.43         8.09        23.90 

$`TP53 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A1 
       11.57         4.27         8.12         8.84         9.99        25.28 
TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
        9.67         3.52        42.84        16.21        15.39 

  TP53 MUTATED TP53 WILD-TYPE 
          1.08           3.52 
  TP53 MUTATED TP53 WILD-TYPE 
         48.79          42.84 
  TP53 MUTATED TP53 WILD-TYPE 
          8.09           9.99 
[1] "1.1 - 48.8 (8.1)"  "3.5 - 42.8 (10.0)"
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" 
[1] "hr=" "1.2"
D2V2, continuous
                vv
clus             DISTANT METASTASIS
  TP53 MUTATED                    1
  TP53 WILD-TYPE                  7
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  TP53 MUTATED                                                                                          1
  TP53 WILD-TYPE                                                                                        8
                vv
clus             REGIONAL LYMPH NODE
  TP53 MUTATED                     7
  TP53 WILD-TYPE                  21
D2V3, multiclass
                                                                                          clus
vv                                                                                         TP53 MUTATED
  DISTANT METASTASIS                                                                                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            1
  REGIONAL LYMPH NODE                                                                                 7
                                                                                          clus
vv                                                                                         TP53 WILD-TYPE
  DISTANT METASTASIS                                                                                    7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              8
  REGIONAL LYMPH NODE                                                                                  21
D2V4, binary
                cls
clus              0  1
  TP53 MUTATED    3  6
  TP53 WILD-TYPE 13 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      3    6
  TP53 WILD-TYPE   13   23
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            3             13
  MALE              6             23
                vv
clus             N0 N1A N1B N2A N2B N3
  TP53 MUTATED    3   2   2   0   1  1
  TP53 WILD-TYPE 24   1   2   1   1  4
D2V5, multiclass
D2V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  TP53 MUTATED             0       1        1        1        0         0
  TP53 WILD-TYPE           1       2        3        5        4         3
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TP53 MUTATED           0         0         0          0          4          2
  TP53 WILD-TYPE         4         2         1          1          2          4
                vv
clus             STAGE IV
  TP53 MUTATED          0
  TP53 WILD-TYPE        1
D2V7, multiclass

Clustering(3) Variable = MUM1L1 MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2               0  1
  MUM1L1 MUTATED    2  2
  MUM1L1 WILD-TYPE  7 11
  MUM1L1 MUTATED MUM1L1 WILD-TYPE 
               4               18 
  MUM1L1 MUTATED MUM1L1 WILD-TYPE 
               2               11 
$`MUM1L1 MUTATED`
TCGA-D3-A3MV TCGA-EE-A29R TCGA-EE-A29V TCGA-GN-A268 
        5.39         8.84         2.43        15.39 

$`MUM1L1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X 
       11.57         4.27         1.08         8.12         9.99         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
       25.28        23.90         9.67         3.52        42.84        16.21 

  MUM1L1 MUTATED MUM1L1 WILD-TYPE 
            2.43             1.08 
  MUM1L1 MUTATED MUM1L1 WILD-TYPE 
           15.39            48.79 
  MUM1L1 MUTATED MUM1L1 WILD-TYPE 
           7.115           10.780 
[1] "2.4 - 15.4 (7.1)"  "1.1 - 48.8 (10.8)"
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE"   "MUM1L1 MUTATED" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE"   "MUM1L1 MUTATED" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"MUM1L1 WILD-TYPE"   "MUM1L1 MUTATED" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"MUM1L1 WILD-TYPE"   "MUM1L1 MUTATED" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE"   "MUM1L1 MUTATED" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE"   "MUM1L1 MUTATED" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"MUM1L1 WILD-TYPE"   "MUM1L1 MUTATED" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"MUM1L1 WILD-TYPE"   "MUM1L1 MUTATED" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE"   "MUM1L1 MUTATED" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE"   "MUM1L1 MUTATED" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"MUM1L1 WILD-TYPE"   "MUM1L1 MUTATED" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" "MUM1L1 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"MUM1L1 WILD-TYPE"   "MUM1L1 MUTATED" 
[1] "hr=" "1.6"
D3V2, continuous
                  vv
clus               DISTANT METASTASIS
  MUM1L1 MUTATED                    3
  MUM1L1 WILD-TYPE                  5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  MUM1L1 MUTATED                                                                                          1
  MUM1L1 WILD-TYPE                                                                                        8
                  vv
clus               REGIONAL LYMPH NODE
  MUM1L1 MUTATED                     3
  MUM1L1 WILD-TYPE                  25
D3V3, multiclass
                                                                                          clus
vv                                                                                         MUM1L1 MUTATED
  DISTANT METASTASIS                                                                                    3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   3
                                                                                          clus
vv                                                                                         MUM1L1 WILD-TYPE
  DISTANT METASTASIS                                                                                      5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    25
D3V4, binary
                  cls
clus                0  1
  MUM1L1 MUTATED    3  4
  MUM1L1 WILD-TYPE 13 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MUM1L1 MUTATED      3    4
  MUM1L1 WILD-TYPE   13   25
        clus
vv       MUM1L1 MUTATED MUM1L1 WILD-TYPE
  FEMALE              3               13
  MALE                4               25
                  vv
clus               N0 N1A N1B N2A N2B N3
  MUM1L1 MUTATED    3   0   3   1   0  0
  MUM1L1 WILD-TYPE 24   3   1   0   2  5
D3V5, multiclass
D3V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  MUM1L1 MUTATED             0       0        0        0        2         0
  MUM1L1 WILD-TYPE           1       3        4        6        2         3
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  MUM1L1 MUTATED           1         0         1          0          1
  MUM1L1 WILD-TYPE         3         2         0          1          5
                  vv
clus               STAGE IIIC STAGE IV
  MUM1L1 MUTATED            2        0
  MUM1L1 WILD-TYPE          4        1
D3V7, multiclass

Clustering(4) Variable = CD163L1 MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  CD163L1 MUTATED    3  2
  CD163L1 WILD-TYPE  6 11
  CD163L1 MUTATED CD163L1 WILD-TYPE 
                5                17 
  CD163L1 MUTATED CD163L1 WILD-TYPE 
                2                11 
$`CD163L1 MUTATED`
TCGA-EE-A29L TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A2 TCGA-ER-A19N 
        1.08         9.99         2.43        23.90        42.84 

$`CD163L1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29X 
        7.00        11.57         4.27         8.12         8.84         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A267 TCGA-GN-A268 
       25.28         9.67         3.52        16.21        15.39 

  CD163L1 MUTATED CD163L1 WILD-TYPE 
             1.08              3.52 
  CD163L1 MUTATED CD163L1 WILD-TYPE 
            42.84             48.79 
  CD163L1 MUTATED CD163L1 WILD-TYPE 
             9.99              9.67 
[1] "1.1 - 42.8 (10.0)" "3.5 - 48.8 (9.7)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"CD163L1 WILD-TYPE"   "CD163L1 MUTATED" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "CD163L1 MUTATED"   "CD163L1 MUTATED" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "CD163L1 MUTATED" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE"   "CD163L1 MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"CD163L1 WILD-TYPE"   "CD163L1 MUTATED" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "CD163L1 MUTATED"   "CD163L1 MUTATED" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "CD163L1 MUTATED" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE"   "CD163L1 MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"CD163L1 WILD-TYPE"   "CD163L1 MUTATED" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "CD163L1 MUTATED"   "CD163L1 MUTATED" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "CD163L1 MUTATED" "CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE"   "CD163L1 MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"CD163L1 WILD-TYPE" "CD163L1 WILD-TYPE" 
[1] "hr=" "1.5"
D4V2, continuous
                   vv
clus                DISTANT METASTASIS
  CD163L1 MUTATED                    2
  CD163L1 WILD-TYPE                  6
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CD163L1 MUTATED                                                                                          2
  CD163L1 WILD-TYPE                                                                                        7
                   vv
clus                REGIONAL LYMPH NODE
  CD163L1 MUTATED                     9
  CD163L1 WILD-TYPE                  19
D4V3, multiclass
                                                                                          clus
vv                                                                                         CD163L1 MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    9
                                                                                          clus
vv                                                                                         CD163L1 WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 7
  REGIONAL LYMPH NODE                                                                                     19
D4V4, binary
                   cls
clus                 0  1
  CD163L1 MUTATED    4  9
  CD163L1 WILD-TYPE 12 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CD163L1 MUTATED      4    9
  CD163L1 WILD-TYPE   12   20
        clus
vv       CD163L1 MUTATED CD163L1 WILD-TYPE
  FEMALE               4                12
  MALE                 9                20
                   vv
clus                N0 N1A N1B N2A N2B N3
  CD163L1 MUTATED    9   0   2   0   0  1
  CD163L1 WILD-TYPE 18   3   2   1   2  4
D4V5, multiclass
D4V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CD163L1 MUTATED             0       2        2        0        1         1
  CD163L1 WILD-TYPE           1       1        2        6        3         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CD163L1 MUTATED           2         1         0          0          1
  CD163L1 WILD-TYPE         2         1         1          1          5
                   vv
clus                STAGE IIIC STAGE IV
  CD163L1 MUTATED            2        0
  CD163L1 WILD-TYPE          4        1
D4V7, multiclass

Clustering(5) Variable = PSG4 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2             0  1
  PSG4 MUTATED    0  2
  PSG4 WILD-TYPE  9 11
  PSG4 MUTATED PSG4 WILD-TYPE 
             2             20 
  PSG4 MUTATED PSG4 WILD-TYPE 
             2             11 
$`PSG4 MUTATED`
TCGA-D3-A2J8 TCGA-EE-A185 
        8.38         4.27 

$`PSG4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       11.57         1.08         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  PSG4 MUTATED PSG4 WILD-TYPE 
          4.27           1.08 
  PSG4 MUTATED PSG4 WILD-TYPE 
          8.38          48.79 
  PSG4 MUTATED PSG4 WILD-TYPE 
         6.325         10.780 
[1] "4.3 - 8.4 (6.3)"   "1.1 - 48.8 (10.8)"
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE"   "PSG4 MUTATED" "PSG4 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
  "PSG4 MUTATED" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE"   "PSG4 MUTATED" "PSG4 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
  "PSG4 MUTATED" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE"   "PSG4 MUTATED" "PSG4 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
  "PSG4 MUTATED" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
[1] "Remove cluster labels:" "PSG4 MUTATED"          
clus
  PSG4 MUTATED PSG4 WILD-TYPE 
             2             20 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A3MV     TCGA-DA-A1HV 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X     TCGA-EE-A29L 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-EE-A29Q     TCGA-EE-A29R     TCGA-EE-A29S     TCGA-EE-A29V 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-EE-A29X     TCGA-EE-A2A1     TCGA-EE-A2A2     TCGA-EE-A2A5 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
    TCGA-ER-A19D     TCGA-ER-A19N     TCGA-GN-A267     TCGA-GN-A268 
"PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" "PSG4 WILD-TYPE" 
D5V2, continuous
                vv
clus             DISTANT METASTASIS
  PSG4 MUTATED                    1
  PSG4 WILD-TYPE                  7
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  PSG4 MUTATED                                                                                          0
  PSG4 WILD-TYPE                                                                                        9
                vv
clus             REGIONAL LYMPH NODE
  PSG4 MUTATED                     7
  PSG4 WILD-TYPE                  21
D5V3, multiclass
                                                                                          clus
vv                                                                                         PSG4 MUTATED
  DISTANT METASTASIS                                                                                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            0
  REGIONAL LYMPH NODE                                                                                 7
                                                                                          clus
vv                                                                                         PSG4 WILD-TYPE
  DISTANT METASTASIS                                                                                    7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              9
  REGIONAL LYMPH NODE                                                                                  21
D5V4, binary
                cls
clus              0  1
  PSG4 MUTATED    4  4
  PSG4 WILD-TYPE 12 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  PSG4 MUTATED      4    4
  PSG4 WILD-TYPE   12   25
        clus
vv       PSG4 MUTATED PSG4 WILD-TYPE
  FEMALE            4             12
  MALE              4             25
                vv
clus             N0 N1A N1B N2A N2B N3
  PSG4 MUTATED    4   1   0   0   0  1
  PSG4 WILD-TYPE 23   2   4   1   2  4
D5V5, multiclass
D5V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  PSG4 MUTATED             0       1        0        1        1         1
  PSG4 WILD-TYPE           1       2        4        5        3         2
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PSG4 MUTATED           0         0         0          0          1          1
  PSG4 WILD-TYPE         4         2         1          1          5          5
                vv
clus             STAGE IV
  PSG4 MUTATED          0
  PSG4 WILD-TYPE        1
D5V7, multiclass

Clustering(6) Variable = PPP6C MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2              0  1
  PPP6C MUTATED    3  2
  PPP6C WILD-TYPE  6 11
  PPP6C MUTATED PPP6C WILD-TYPE 
              5              17 
  PPP6C MUTATED PPP6C WILD-TYPE 
              2              11 
$`PPP6C MUTATED`
TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-EE-A29L TCGA-EE-A29R TCGA-GN-A267 
        5.39        39.19         1.08         8.84        16.21 

$`PPP6C WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A3F3 TCGA-EE-A17X 
       16.47        28.08         8.38        48.79         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
        4.27         8.12         9.99         2.43         8.09        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A268 
       23.90         9.67         3.52        42.84        15.39 

  PPP6C MUTATED PPP6C WILD-TYPE 
           1.08            2.43 
  PPP6C MUTATED PPP6C WILD-TYPE 
          39.19           48.79 
  PPP6C MUTATED PPP6C WILD-TYPE 
           8.84            9.99 
[1] "1.1 - 39.2 (8.8)"  "2.4 - 48.8 (10.0)"
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE"   "PPP6C MUTATED" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"PPP6C WILD-TYPE"   "PPP6C MUTATED" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"PPP6C WILD-TYPE"   "PPP6C MUTATED" "PPP6C WILD-TYPE"   "PPP6C MUTATED" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
  "PPP6C MUTATED" "PPP6C WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE"   "PPP6C MUTATED" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"PPP6C WILD-TYPE"   "PPP6C MUTATED" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"PPP6C WILD-TYPE"   "PPP6C MUTATED" "PPP6C WILD-TYPE"   "PPP6C MUTATED" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
  "PPP6C MUTATED" "PPP6C WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE"   "PPP6C MUTATED" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"PPP6C WILD-TYPE"   "PPP6C MUTATED" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"PPP6C WILD-TYPE"   "PPP6C MUTATED" "PPP6C WILD-TYPE"   "PPP6C MUTATED" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
  "PPP6C MUTATED" "PPP6C WILD-TYPE" 
[1] "hr=" "1.4"
D6V2, continuous
                 vv
clus              DISTANT METASTASIS
  PPP6C MUTATED                    0
  PPP6C WILD-TYPE                  8
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  PPP6C MUTATED                                                                                          4
  PPP6C WILD-TYPE                                                                                        5
                 vv
clus              REGIONAL LYMPH NODE
  PPP6C MUTATED                     5
  PPP6C WILD-TYPE                  23
D6V3, multiclass
                                                                                          clus
vv                                                                                         PPP6C MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             4
  REGIONAL LYMPH NODE                                                                                  5
                                                                                          clus
vv                                                                                         PPP6C WILD-TYPE
  DISTANT METASTASIS                                                                                     8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                   23
D6V4, binary
                 cls
clus               0  1
  PPP6C MUTATED    4  5
  PPP6C WILD-TYPE 12 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPP6C MUTATED      4    5
  PPP6C WILD-TYPE   12   24
        clus
vv       PPP6C MUTATED PPP6C WILD-TYPE
  FEMALE             4              12
  MALE               5              24
                 vv
clus              N0 N1A N1B N2A N2B N3
  PPP6C MUTATED    3   2   1   1   0  2
  PPP6C WILD-TYPE 24   1   3   0   2  3
D6V5, multiclass
D6V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  PPP6C MUTATED             0       0        0        0        1         0
  PPP6C WILD-TYPE           1       3        4        6        3         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  PPP6C MUTATED           1         1         0          1          2
  PPP6C WILD-TYPE         3         1         1          0          4
                 vv
clus              STAGE IIIC STAGE IV
  PPP6C MUTATED            3        0
  PPP6C WILD-TYPE          3        1
D6V7, multiclass

Clustering(7) Variable = ZNF99 MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2             0 1
  ZNF99 MUTATED   2 5
  ZNF99 WILD-TYPE 7 8
  ZNF99 MUTATED ZNF99 WILD-TYPE 
              7              15 
  ZNF99 MUTATED ZNF99 WILD-TYPE 
              5               8 
$`ZNF99 MUTATED`
TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29V 
        8.38        48.79        11.57         1.08         8.84         2.43 
TCGA-ER-A19D 
        3.52 

$`ZNF99 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A185 
       16.47        28.08         5.39        39.19         7.00         4.27 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.12         9.99         8.09        25.28        23.90         9.67 
TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       42.84        16.21        15.39 

  ZNF99 MUTATED ZNF99 WILD-TYPE 
           1.08            4.27 
  ZNF99 MUTATED ZNF99 WILD-TYPE 
          48.79           42.84 
  ZNF99 MUTATED ZNF99 WILD-TYPE 
           8.38           15.39 
[1] "1.1 - 48.8 (8.4)"  "4.3 - 42.8 (15.4)"
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ZNF99 WILD-TYPE" "ZNF99 WILD-TYPE"   "ZNF99 MUTATED" "ZNF99 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "ZNF99 MUTATED" "ZNF99 WILD-TYPE" "ZNF99 WILD-TYPE"   "ZNF99 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ZNF99 WILD-TYPE"   "ZNF99 MUTATED" "ZNF99 WILD-TYPE"   "ZNF99 MUTATED" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"ZNF99 WILD-TYPE"   "ZNF99 MUTATED" "ZNF99 WILD-TYPE" "ZNF99 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"ZNF99 WILD-TYPE" "ZNF99 WILD-TYPE"   "ZNF99 MUTATED" "ZNF99 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ZNF99 WILD-TYPE" "ZNF99 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ZNF99 WILD-TYPE" "ZNF99 WILD-TYPE"   "ZNF99 MUTATED" "ZNF99 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "ZNF99 MUTATED" "ZNF99 WILD-TYPE" "ZNF99 WILD-TYPE"   "ZNF99 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ZNF99 WILD-TYPE"   "ZNF99 MUTATED" "ZNF99 WILD-TYPE"   "ZNF99 MUTATED" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"ZNF99 WILD-TYPE"   "ZNF99 MUTATED" "ZNF99 WILD-TYPE" "ZNF99 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"ZNF99 WILD-TYPE" "ZNF99 WILD-TYPE"   "ZNF99 MUTATED" "ZNF99 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ZNF99 WILD-TYPE" "ZNF99 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ZNF99 WILD-TYPE" "ZNF99 WILD-TYPE"   "ZNF99 MUTATED" "ZNF99 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "ZNF99 MUTATED" "ZNF99 WILD-TYPE" "ZNF99 WILD-TYPE"   "ZNF99 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ZNF99 WILD-TYPE"   "ZNF99 MUTATED" "ZNF99 WILD-TYPE"   "ZNF99 MUTATED" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"ZNF99 WILD-TYPE"   "ZNF99 MUTATED" "ZNF99 WILD-TYPE" "ZNF99 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"ZNF99 WILD-TYPE" "ZNF99 WILD-TYPE"   "ZNF99 MUTATED" "ZNF99 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ZNF99 WILD-TYPE" "ZNF99 WILD-TYPE" 
[1] "hr=" "2.3"
D7V2, continuous
                 vv
clus              DISTANT METASTASIS
  ZNF99 MUTATED                    3
  ZNF99 WILD-TYPE                  5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ZNF99 MUTATED                                                                                          1
  ZNF99 WILD-TYPE                                                                                        8
                 vv
clus              REGIONAL LYMPH NODE
  ZNF99 MUTATED                     9
  ZNF99 WILD-TYPE                  19
D7V3, multiclass
                                                                                          clus
vv                                                                                         ZNF99 MUTATED
  DISTANT METASTASIS                                                                                   3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  9
                                                                                          clus
vv                                                                                         ZNF99 WILD-TYPE
  DISTANT METASTASIS                                                                                     5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               8
  REGIONAL LYMPH NODE                                                                                   19
D7V4, binary
                 cls
clus               0  1
  ZNF99 MUTATED    6  7
  ZNF99 WILD-TYPE 10 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF99 MUTATED      6    7
  ZNF99 WILD-TYPE   10   22
        clus
vv       ZNF99 MUTATED ZNF99 WILD-TYPE
  FEMALE             6              10
  MALE               7              22
                 vv
clus              N0 N1A N1B N2A N2B N3
  ZNF99 MUTATED    8   0   2   0   1  1
  ZNF99 WILD-TYPE 19   3   2   1   1  4
D7V5, multiclass
D7V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ZNF99 MUTATED             0       2        2        2        2         0
  ZNF99 WILD-TYPE           1       1        2        4        2         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ZNF99 MUTATED           0         0         0          0          1
  ZNF99 WILD-TYPE         4         2         1          1          5
                 vv
clus              STAGE IIIC STAGE IV
  ZNF99 MUTATED            3        0
  ZNF99 WILD-TYPE          3        1
D7V7, multiclass

Clustering(8) Variable = KHDRBS2 MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  KHDRBS2 MUTATED    3  1
  KHDRBS2 WILD-TYPE  6 12
  KHDRBS2 MUTATED KHDRBS2 WILD-TYPE 
                4                18 
  KHDRBS2 MUTATED KHDRBS2 WILD-TYPE 
                1                12 
$`KHDRBS2 MUTATED`
TCGA-DA-A1HV TCGA-EE-A29L TCGA-EE-A29S TCGA-EE-A2A2 
       48.79         1.08         9.99        23.90 

$`KHDRBS2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29X 
       11.57         4.27         8.12         8.84         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       25.28         9.67         3.52        42.84        16.21        15.39 

  KHDRBS2 MUTATED KHDRBS2 WILD-TYPE 
             1.08              2.43 
  KHDRBS2 MUTATED KHDRBS2 WILD-TYPE 
            48.79             42.84 
  KHDRBS2 MUTATED KHDRBS2 WILD-TYPE 
           16.945             9.255 
[1] "1.1 - 48.8 (16.9)" "2.4 - 42.8 (9.3)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "KHDRBS2 MUTATED" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"KHDRBS2 WILD-TYPE"   "KHDRBS2 MUTATED" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "KHDRBS2 MUTATED" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "KHDRBS2 MUTATED" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "KHDRBS2 MUTATED" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"KHDRBS2 WILD-TYPE"   "KHDRBS2 MUTATED" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "KHDRBS2 MUTATED" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "KHDRBS2 MUTATED" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "KHDRBS2 MUTATED" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"KHDRBS2 WILD-TYPE"   "KHDRBS2 MUTATED" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "KHDRBS2 MUTATED" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "KHDRBS2 MUTATED" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"KHDRBS2 WILD-TYPE" "KHDRBS2 WILD-TYPE" 
[1] "hr=" "3.1"
D8V2, continuous
                   vv
clus                DISTANT METASTASIS
  KHDRBS2 MUTATED                    1
  KHDRBS2 WILD-TYPE                  7
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  KHDRBS2 MUTATED                                                                                          0
  KHDRBS2 WILD-TYPE                                                                                        9
                   vv
clus                REGIONAL LYMPH NODE
  KHDRBS2 MUTATED                     7
  KHDRBS2 WILD-TYPE                  21
D8V3, multiclass
                                                                                          clus
vv                                                                                         KHDRBS2 MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    7
                                                                                          clus
vv                                                                                         KHDRBS2 WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 9
  REGIONAL LYMPH NODE                                                                                     21
D8V4, binary
                   cls
clus                 0  1
  KHDRBS2 MUTATED    2  6
  KHDRBS2 WILD-TYPE 14 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KHDRBS2 MUTATED      2    6
  KHDRBS2 WILD-TYPE   14   23
        clus
vv       KHDRBS2 MUTATED KHDRBS2 WILD-TYPE
  FEMALE               2                14
  MALE                 6                23
                   vv
clus                N0 N1A N1B N2A N2B N3
  KHDRBS2 MUTATED    4   0   1   0   1  1
  KHDRBS2 WILD-TYPE 23   3   3   1   1  4
D8V5, multiclass
D8V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  KHDRBS2 MUTATED             0       1        0        0        2         1
  KHDRBS2 WILD-TYPE           1       2        4        6        2         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  KHDRBS2 MUTATED           0         0         0          0          2
  KHDRBS2 WILD-TYPE         4         2         1          1          4
                   vv
clus                STAGE IIIC STAGE IV
  KHDRBS2 MUTATED            1        0
  KHDRBS2 WILD-TYPE          5        1
D8V7, multiclass

Clustering(9) Variable = POTEG MUTATION ANALYSIS
D9V1, survival
                 sevent
clus2             0 1
  POTEG MUTATED   2 4
  POTEG WILD-TYPE 7 9
  POTEG MUTATED POTEG WILD-TYPE 
              6              16 
  POTEG MUTATED POTEG WILD-TYPE 
              4               9 
$`POTEG MUTATED`
TCGA-DA-A1HV TCGA-EE-A29L TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A5 TCGA-ER-A19D 
       48.79         1.08         9.99         2.43         9.67         3.52 

$`POTEG WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29X TCGA-EE-A2A1 
       11.57         4.27         8.12         8.84         8.09        25.28 
TCGA-EE-A2A2 TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       23.90        42.84        16.21        15.39 

  POTEG MUTATED POTEG WILD-TYPE 
           1.08            4.27 
  POTEG MUTATED POTEG WILD-TYPE 
          48.79           42.84 
  POTEG MUTATED POTEG WILD-TYPE 
          6.595          13.480 
[1] "1.1 - 48.8 (6.6)"  "4.3 - 42.8 (13.5)"
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"POTEG WILD-TYPE" "POTEG WILD-TYPE" "POTEG WILD-TYPE" "POTEG WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "POTEG MUTATED" "POTEG WILD-TYPE" "POTEG WILD-TYPE" "POTEG WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"POTEG WILD-TYPE"   "POTEG MUTATED" "POTEG WILD-TYPE" "POTEG WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "POTEG MUTATED"   "POTEG MUTATED" "POTEG WILD-TYPE" "POTEG WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"POTEG WILD-TYPE"   "POTEG MUTATED"   "POTEG MUTATED" "POTEG WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"POTEG WILD-TYPE" "POTEG WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"POTEG WILD-TYPE" "POTEG WILD-TYPE" "POTEG WILD-TYPE" "POTEG WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "POTEG MUTATED" "POTEG WILD-TYPE" "POTEG WILD-TYPE" "POTEG WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"POTEG WILD-TYPE"   "POTEG MUTATED" "POTEG WILD-TYPE" "POTEG WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "POTEG MUTATED"   "POTEG MUTATED" "POTEG WILD-TYPE" "POTEG WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"POTEG WILD-TYPE"   "POTEG MUTATED"   "POTEG MUTATED" "POTEG WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"POTEG WILD-TYPE" "POTEG WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"POTEG WILD-TYPE" "POTEG WILD-TYPE" "POTEG WILD-TYPE" "POTEG WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "POTEG MUTATED" "POTEG WILD-TYPE" "POTEG WILD-TYPE" "POTEG WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"POTEG WILD-TYPE"   "POTEG MUTATED" "POTEG WILD-TYPE" "POTEG WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "POTEG MUTATED"   "POTEG MUTATED" "POTEG WILD-TYPE" "POTEG WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"POTEG WILD-TYPE"   "POTEG MUTATED"   "POTEG MUTATED" "POTEG WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"POTEG WILD-TYPE" "POTEG WILD-TYPE" 
[1] "hr=" "2"  
D9V2, continuous
                 vv
clus              DISTANT METASTASIS
  POTEG MUTATED                    2
  POTEG WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  POTEG MUTATED                                                                                          2
  POTEG WILD-TYPE                                                                                        7
                 vv
clus              REGIONAL LYMPH NODE
  POTEG MUTATED                     4
  POTEG WILD-TYPE                  24
D9V3, multiclass
                                                                                          clus
vv                                                                                         POTEG MUTATED
  DISTANT METASTASIS                                                                                   2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  4
                                                                                          clus
vv                                                                                         POTEG WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   24
D9V4, binary
                 cls
clus               0  1
  POTEG MUTATED    2  6
  POTEG WILD-TYPE 14 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED      2    6
  POTEG WILD-TYPE   14   23
        clus
vv       POTEG MUTATED POTEG WILD-TYPE
  FEMALE             2              14
  MALE               6              23
                 vv
clus              N0 N1A N1B N2A N2B N3
  POTEG MUTATED    4   0   2   0   1  1
  POTEG WILD-TYPE 23   3   2   1   1  4
D9V5, multiclass
D9V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  POTEG MUTATED             0       0        0        2        1         1
  POTEG WILD-TYPE           1       3        4        4        3         2
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  POTEG MUTATED           0         0         1          0          1
  POTEG WILD-TYPE         4         2         0          1          5
                 vv
clus              STAGE IIIC STAGE IV
  POTEG MUTATED            2        0
  POTEG WILD-TYPE          4        1
D9V7, multiclass

Clustering(10) Variable = MARCO MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2              0  1
  MARCO MUTATED    3  2
  MARCO WILD-TYPE  6 11
  MARCO MUTATED MARCO WILD-TYPE 
              5              17 
  MARCO MUTATED MARCO WILD-TYPE 
              2              11 
$`MARCO MUTATED`
TCGA-D3-A1Q8 TCGA-EE-A185 TCGA-EE-A29S TCGA-EE-A2A1 TCGA-EE-A2A2 
       28.08         4.27         9.99        25.28        23.90 

$`MARCO WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47         8.38         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29X 
       11.57         1.08         8.12         8.84         2.43         8.09 
TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
        9.67         3.52        42.84        16.21        15.39 

  MARCO MUTATED MARCO WILD-TYPE 
           4.27            1.08 
  MARCO MUTATED MARCO WILD-TYPE 
          28.08           48.79 
  MARCO MUTATED MARCO WILD-TYPE 
          23.90            8.84 
[1] "4.3 - 28.1 (23.9)" "1.1 - 48.8 (8.8)" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"MARCO WILD-TYPE"   "MARCO MUTATED" "MARCO WILD-TYPE" "MARCO WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"MARCO WILD-TYPE" "MARCO WILD-TYPE" "MARCO WILD-TYPE" "MARCO WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
  "MARCO MUTATED" "MARCO WILD-TYPE" "MARCO WILD-TYPE" "MARCO WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "MARCO MUTATED" "MARCO WILD-TYPE" "MARCO WILD-TYPE"   "MARCO MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "MARCO MUTATED" "MARCO WILD-TYPE" "MARCO WILD-TYPE" "MARCO WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"MARCO WILD-TYPE" "MARCO WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"MARCO WILD-TYPE"   "MARCO MUTATED" "MARCO WILD-TYPE" "MARCO WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"MARCO WILD-TYPE" "MARCO WILD-TYPE" "MARCO WILD-TYPE" "MARCO WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
  "MARCO MUTATED" "MARCO WILD-TYPE" "MARCO WILD-TYPE" "MARCO WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "MARCO MUTATED" "MARCO WILD-TYPE" "MARCO WILD-TYPE"   "MARCO MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "MARCO MUTATED" "MARCO WILD-TYPE" "MARCO WILD-TYPE" "MARCO WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"MARCO WILD-TYPE" "MARCO WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"MARCO WILD-TYPE"   "MARCO MUTATED" "MARCO WILD-TYPE" "MARCO WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"MARCO WILD-TYPE" "MARCO WILD-TYPE" "MARCO WILD-TYPE" "MARCO WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
  "MARCO MUTATED" "MARCO WILD-TYPE" "MARCO WILD-TYPE" "MARCO WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "MARCO MUTATED" "MARCO WILD-TYPE" "MARCO WILD-TYPE"   "MARCO MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "MARCO MUTATED" "MARCO WILD-TYPE" "MARCO WILD-TYPE" "MARCO WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"MARCO WILD-TYPE" "MARCO WILD-TYPE" 
[1] "hr=" "2.3"
D10V2, continuous
                 vv
clus              DISTANT METASTASIS
  MARCO MUTATED                    0
  MARCO WILD-TYPE                  8
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  MARCO MUTATED                                                                                          1
  MARCO WILD-TYPE                                                                                        8
                 vv
clus              REGIONAL LYMPH NODE
  MARCO MUTATED                     8
  MARCO WILD-TYPE                  20
D10V3, multiclass
                                                                                          clus
vv                                                                                         MARCO MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  8
                                                                                          clus
vv                                                                                         MARCO WILD-TYPE
  DISTANT METASTASIS                                                                                     8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               8
  REGIONAL LYMPH NODE                                                                                   20
D10V4, binary
                 cls
clus               0  1
  MARCO MUTATED    1  8
  MARCO WILD-TYPE 15 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MARCO MUTATED      1    8
  MARCO WILD-TYPE   15   21
        clus
vv       MARCO MUTATED MARCO WILD-TYPE
  FEMALE             1              15
  MALE               8              21
                 vv
clus              N0 N1A N1B N2A N2B N3
  MARCO MUTATED    4   2   1   0   0  2
  MARCO WILD-TYPE 23   1   3   1   2  3
D10V5, multiclass
D10V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  MARCO MUTATED             0       0        0        1        2         1
  MARCO WILD-TYPE           1       3        4        5        2         2
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  MARCO MUTATED           0         0         0          0          3
  MARCO WILD-TYPE         4         2         1          1          3
                 vv
clus              STAGE IIIC STAGE IV
  MARCO MUTATED            1        1
  MARCO WILD-TYPE          5        0
D10V7, multiclass

Clustering(11) Variable = SGCZ MUTATION ANALYSIS
D11V1, survival
                sevent
clus2             0  1
  SGCZ MUTATED    3  0
  SGCZ WILD-TYPE  6 13
  SGCZ MUTATED SGCZ WILD-TYPE 
             3             19 
  SGCZ MUTATED SGCZ WILD-TYPE 
             0             13 
$`SGCZ MUTATED`
TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-EE-A29R 
        5.39        39.19         8.84 

$`SGCZ WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A3F3 TCGA-EE-A17X 
       16.47        28.08         8.38        48.79         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
        4.27         1.08         8.12         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
       25.28        23.90         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  SGCZ MUTATED SGCZ WILD-TYPE 
          5.39           1.08 
  SGCZ MUTATED SGCZ WILD-TYPE 
         39.19          48.79 
  SGCZ MUTATED SGCZ WILD-TYPE 
          8.84           9.99 
[1] "5.4 - 39.2 (8.8)"  "1.1 - 48.8 (10.0)"
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE"   "SGCZ MUTATED" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"SGCZ WILD-TYPE"   "SGCZ MUTATED" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE"   "SGCZ MUTATED" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"SGCZ WILD-TYPE" "SGCZ WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE"   "SGCZ MUTATED" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"SGCZ WILD-TYPE"   "SGCZ MUTATED" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE"   "SGCZ MUTATED" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"SGCZ WILD-TYPE" "SGCZ WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE"   "SGCZ MUTATED" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"SGCZ WILD-TYPE"   "SGCZ MUTATED" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE"   "SGCZ MUTATED" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE" "SGCZ WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"SGCZ WILD-TYPE" "SGCZ WILD-TYPE" 
[1] "hr="     "2.3e+08"
D11V2, continuous
                vv
clus             DISTANT METASTASIS
  SGCZ MUTATED                    2
  SGCZ WILD-TYPE                  6
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  SGCZ MUTATED                                                                                          2
  SGCZ WILD-TYPE                                                                                        7
                vv
clus             REGIONAL LYMPH NODE
  SGCZ MUTATED                     4
  SGCZ WILD-TYPE                  24
D11V3, multiclass
                                                                                          clus
vv                                                                                         SGCZ MUTATED
  DISTANT METASTASIS                                                                                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            2
  REGIONAL LYMPH NODE                                                                                 4
                                                                                          clus
vv                                                                                         SGCZ WILD-TYPE
  DISTANT METASTASIS                                                                                    6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              7
  REGIONAL LYMPH NODE                                                                                  24
D11V4, binary
                cls
clus              0  1
  SGCZ MUTATED    3  5
  SGCZ WILD-TYPE 13 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGCZ MUTATED      3    5
  SGCZ WILD-TYPE   13   24
        clus
vv       SGCZ MUTATED SGCZ WILD-TYPE
  FEMALE            3             13
  MALE              5             24
                vv
clus             N0 N1A N1B N2A N2B N3
  SGCZ MUTATED    4   0   1   1   0  1
  SGCZ WILD-TYPE 23   3   3   0   2  4
D11V5, multiclass
D11V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  SGCZ MUTATED             1       1        1        0        1         0
  SGCZ WILD-TYPE           0       2        3        6        3         3
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SGCZ MUTATED           0         0         0          0          1          2
  SGCZ WILD-TYPE         4         2         1          1          5          4
                vv
clus             STAGE IV
  SGCZ MUTATED          0
  SGCZ WILD-TYPE        1
D11V7, multiclass

Clustering(12) Variable = GLRB MUTATION ANALYSIS
D12V1, survival
                sevent
clus2             0  1
  GLRB MUTATED    0  3
  GLRB WILD-TYPE  9 10
  GLRB MUTATED GLRB WILD-TYPE 
             3             19 
  GLRB MUTATED GLRB WILD-TYPE 
             3             10 
$`GLRB MUTATED`
TCGA-D3-A2J8 TCGA-EE-A29L TCGA-ER-A19D 
        8.38         1.08         3.52 

$`GLRB WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       11.57         4.27         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19N TCGA-GN-A267 
        8.09        25.28        23.90         9.67        42.84        16.21 
TCGA-GN-A268 
       15.39 

  GLRB MUTATED GLRB WILD-TYPE 
          1.08           2.43 
  GLRB MUTATED GLRB WILD-TYPE 
          8.38          48.79 
  GLRB MUTATED GLRB WILD-TYPE 
          3.52          11.57 
[1] "1.1 - 8.4 (3.5)"   "2.4 - 48.8 (11.6)"
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"GLRB WILD-TYPE" "GLRB WILD-TYPE"   "GLRB MUTATED" "GLRB WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"GLRB WILD-TYPE"   "GLRB MUTATED" "GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"GLRB WILD-TYPE" "GLRB WILD-TYPE"   "GLRB MUTATED" "GLRB WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"GLRB WILD-TYPE" "GLRB WILD-TYPE"   "GLRB MUTATED" "GLRB WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"GLRB WILD-TYPE"   "GLRB MUTATED" "GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"GLRB WILD-TYPE" "GLRB WILD-TYPE"   "GLRB MUTATED" "GLRB WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"GLRB WILD-TYPE" "GLRB WILD-TYPE"   "GLRB MUTATED" "GLRB WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"GLRB WILD-TYPE"   "GLRB MUTATED" "GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" "GLRB WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"GLRB WILD-TYPE" "GLRB WILD-TYPE"   "GLRB MUTATED" "GLRB WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"GLRB WILD-TYPE" "GLRB WILD-TYPE" 
[1] "hr=" "8.7"
D12V2, continuous
                vv
clus             DISTANT METASTASIS
  GLRB MUTATED                    2
  GLRB WILD-TYPE                  6
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  GLRB MUTATED                                                                                          3
  GLRB WILD-TYPE                                                                                        6
                vv
clus             REGIONAL LYMPH NODE
  GLRB MUTATED                     4
  GLRB WILD-TYPE                  24
D12V3, multiclass
                                                                                          clus
vv                                                                                         GLRB MUTATED
  DISTANT METASTASIS                                                                                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            3
  REGIONAL LYMPH NODE                                                                                 4
                                                                                          clus
vv                                                                                         GLRB WILD-TYPE
  DISTANT METASTASIS                                                                                    6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              6
  REGIONAL LYMPH NODE                                                                                  24
D12V4, binary
                cls
clus              0  1
  GLRB MUTATED    2  7
  GLRB WILD-TYPE 14 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLRB MUTATED      2    7
  GLRB WILD-TYPE   14   22
        clus
vv       GLRB MUTATED GLRB WILD-TYPE
  FEMALE            2             14
  MALE              7             22
                vv
clus             N0 N1A N1B N2A N2B N3
  GLRB MUTATED    7   1   0   0   0  1
  GLRB WILD-TYPE 20   2   4   1   2  4
D12V5, multiclass
D12V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  GLRB MUTATED             1       0        0        3        1         0
  GLRB WILD-TYPE           0       3        4        3        3         3
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  GLRB MUTATED           1         1         0          0          1          1
  GLRB WILD-TYPE         3         1         1          1          5          5
                vv
clus             STAGE IV
  GLRB MUTATED          0
  GLRB WILD-TYPE        1
D12V7, multiclass

Clustering(13) Variable = OR2W1 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2              0  1
  OR2W1 MUTATED    3  0
  OR2W1 WILD-TYPE  6 13
  OR2W1 MUTATED OR2W1 WILD-TYPE 
              3              19 
  OR2W1 MUTATED OR2W1 WILD-TYPE 
              0              13 
$`OR2W1 MUTATED`
TCGA-DA-A1HV TCGA-EE-A2A1 TCGA-EE-A2A2 
       48.79        25.28        23.90 

$`OR2W1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
        2.43         8.09         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  OR2W1 MUTATED OR2W1 WILD-TYPE 
          23.90            1.08 
  OR2W1 MUTATED OR2W1 WILD-TYPE 
          48.79           42.84 
  OR2W1 MUTATED OR2W1 WILD-TYPE 
          25.28            8.84 
[1] "23.9 - 48.8 (25.3)" "1.1 - 42.8 (8.8)"  
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "OR2W1 MUTATED" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE"   "OR2W1 MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "OR2W1 MUTATED" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "OR2W1 MUTATED" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE"   "OR2W1 MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "OR2W1 MUTATED" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "OR2W1 MUTATED" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE"   "OR2W1 MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "OR2W1 MUTATED" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"OR2W1 WILD-TYPE" "OR2W1 WILD-TYPE" 
[1] "hr="     "3.1e+08"
D13V2, continuous
                 vv
clus              DISTANT METASTASIS
  OR2W1 MUTATED                    0
  OR2W1 WILD-TYPE                  8
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  OR2W1 MUTATED                                                                                          1
  OR2W1 WILD-TYPE                                                                                        8
                 vv
clus              REGIONAL LYMPH NODE
  OR2W1 MUTATED                     5
  OR2W1 WILD-TYPE                  23
D13V3, multiclass
                                                                                          clus
vv                                                                                         OR2W1 MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  5
                                                                                          clus
vv                                                                                         OR2W1 WILD-TYPE
  DISTANT METASTASIS                                                                                     8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               8
  REGIONAL LYMPH NODE                                                                                   23
D13V4, binary
                 cls
clus               0  1
  OR2W1 MUTATED    2  4
  OR2W1 WILD-TYPE 14 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2W1 MUTATED      2    4
  OR2W1 WILD-TYPE   14   25
        clus
vv       OR2W1 MUTATED OR2W1 WILD-TYPE
  FEMALE             2              14
  MALE               4              25
                 vv
clus              N0 N1A N1B N2A N2B N3
  OR2W1 MUTATED    3   1   1   0   1  0
  OR2W1 WILD-TYPE 24   2   3   1   1  5
D13V5, multiclass
D13V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  OR2W1 MUTATED             0       0        0        1        1         0
  OR2W1 WILD-TYPE           1       3        4        5        3         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  OR2W1 MUTATED           1         0         0          0          3
  OR2W1 WILD-TYPE         3         2         1          1          3
                 vv
clus              STAGE IIIC STAGE IV
  OR2W1 MUTATED            0        0
  OR2W1 WILD-TYPE          6        1
D13V7, multiclass

Clustering(14) Variable = C4ORF22 MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  C4ORF22 MUTATED    2  1
  C4ORF22 WILD-TYPE  7 12
  C4ORF22 MUTATED C4ORF22 WILD-TYPE 
                3                19 
  C4ORF22 MUTATED C4ORF22 WILD-TYPE 
                1                12 
$`C4ORF22 MUTATED`
TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A2A1 
        1.08         8.84        25.28 

$`C4ORF22 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
        7.00        11.57         4.27         8.12         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
        8.09        23.90         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  C4ORF22 MUTATED C4ORF22 WILD-TYPE 
             1.08              2.43 
  C4ORF22 MUTATED C4ORF22 WILD-TYPE 
            25.28             48.79 
  C4ORF22 MUTATED C4ORF22 WILD-TYPE 
             8.84              9.99 
[1] "1.1 - 25.3 (8.8)"  "2.4 - 48.8 (10.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"C4ORF22 WILD-TYPE"   "C4ORF22 MUTATED" "C4ORF22 WILD-TYPE"   "C4ORF22 MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE"   "C4ORF22 MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"C4ORF22 WILD-TYPE"   "C4ORF22 MUTATED" "C4ORF22 WILD-TYPE"   "C4ORF22 MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE"   "C4ORF22 MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"C4ORF22 WILD-TYPE"   "C4ORF22 MUTATED" "C4ORF22 WILD-TYPE"   "C4ORF22 MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE"   "C4ORF22 MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"C4ORF22 WILD-TYPE" "C4ORF22 WILD-TYPE" 
[1] "hr=" "1.4"
D14V2, continuous
                   vv
clus                DISTANT METASTASIS
  C4ORF22 MUTATED                    1
  C4ORF22 WILD-TYPE                  7
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  C4ORF22 MUTATED                                                                                          0
  C4ORF22 WILD-TYPE                                                                                        9
                   vv
clus                REGIONAL LYMPH NODE
  C4ORF22 MUTATED                     4
  C4ORF22 WILD-TYPE                  24
D14V3, multiclass
                                                                                          clus
vv                                                                                         C4ORF22 MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         C4ORF22 WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 9
  REGIONAL LYMPH NODE                                                                                     24
D14V4, binary
                   cls
clus                 0  1
  C4ORF22 MUTATED    2  3
  C4ORF22 WILD-TYPE 14 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF22 MUTATED      2    3
  C4ORF22 WILD-TYPE   14   26
        clus
vv       C4ORF22 MUTATED C4ORF22 WILD-TYPE
  FEMALE               2                14
  MALE                 3                26
                   vv
clus                N0 N1A N1B N2A N2B N3
  C4ORF22 MUTATED    2   0   1   0   0  1
  C4ORF22 WILD-TYPE 25   3   3   1   2  4
D14V5, multiclass
D14V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  C4ORF22 MUTATED             0       0        0        1        1         0
  C4ORF22 WILD-TYPE           1       3        4        5        3         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  C4ORF22 MUTATED           0         0         0          0          0
  C4ORF22 WILD-TYPE         4         2         1          1          6
                   vv
clus                STAGE IIIC STAGE IV
  C4ORF22 MUTATED            2        0
  C4ORF22 WILD-TYPE          4        1
D14V7, multiclass

Clustering(15) Variable = UGT2B28 MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  UGT2B28 MUTATED    1  3
  UGT2B28 WILD-TYPE  8 10
  UGT2B28 MUTATED UGT2B28 WILD-TYPE 
                4                18 
  UGT2B28 MUTATED UGT2B28 WILD-TYPE 
                3                10 
$`UGT2B28 MUTATED`
TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29X 
       48.79        11.57         1.08         8.09 

$`UGT2B28 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 
        4.27         8.12         8.84         9.99         2.43        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       23.90         9.67         3.52        42.84        16.21        15.39 

  UGT2B28 MUTATED UGT2B28 WILD-TYPE 
             1.08              2.43 
  UGT2B28 MUTATED UGT2B28 WILD-TYPE 
            48.79             42.84 
  UGT2B28 MUTATED UGT2B28 WILD-TYPE 
             9.83              9.83 
[1] "1.1 - 48.8 (9.8)" "2.4 - 42.8 (9.8)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "UGT2B28 MUTATED" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE"   "UGT2B28 MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"UGT2B28 WILD-TYPE"   "UGT2B28 MUTATED" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE"   "UGT2B28 MUTATED" "UGT2B28 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "UGT2B28 MUTATED" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE"   "UGT2B28 MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"UGT2B28 WILD-TYPE"   "UGT2B28 MUTATED" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE"   "UGT2B28 MUTATED" "UGT2B28 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "UGT2B28 MUTATED" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE"   "UGT2B28 MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"UGT2B28 WILD-TYPE"   "UGT2B28 MUTATED" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE"   "UGT2B28 MUTATED" "UGT2B28 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"UGT2B28 WILD-TYPE" "UGT2B28 WILD-TYPE" 
[1] "hr=" "1.5"
D15V2, continuous
                   vv
clus                DISTANT METASTASIS
  UGT2B28 MUTATED                    1
  UGT2B28 WILD-TYPE                  7
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  UGT2B28 MUTATED                                                                                          1
  UGT2B28 WILD-TYPE                                                                                        8
                   vv
clus                REGIONAL LYMPH NODE
  UGT2B28 MUTATED                     6
  UGT2B28 WILD-TYPE                  22
D15V3, multiclass
                                                                                          clus
vv                                                                                         UGT2B28 MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    6
                                                                                          clus
vv                                                                                         UGT2B28 WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 8
  REGIONAL LYMPH NODE                                                                                     22
D15V4, binary
                   cls
clus                 0  1
  UGT2B28 MUTATED    3  5
  UGT2B28 WILD-TYPE 13 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  UGT2B28 MUTATED      3    5
  UGT2B28 WILD-TYPE   13   24
        clus
vv       UGT2B28 MUTATED UGT2B28 WILD-TYPE
  FEMALE               3                13
  MALE                 5                24
                   vv
clus                N0 N1A N1B N2A N2B N3
  UGT2B28 MUTATED    5   0   0   0   1  1
  UGT2B28 WILD-TYPE 22   3   4   1   1  4
D15V5, multiclass
D15V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  UGT2B28 MUTATED             0       0        2        1        1         1
  UGT2B28 WILD-TYPE           1       3        2        5        3         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  UGT2B28 MUTATED           0         0         0          0          1
  UGT2B28 WILD-TYPE         4         2         1          1          5
                   vv
clus                STAGE IIIC STAGE IV
  UGT2B28 MUTATED            1        0
  UGT2B28 WILD-TYPE          5        1
D15V7, multiclass

Clustering(16) Variable = ZNF676 MUTATION ANALYSIS
D16V1, survival
                  sevent
clus2               0  1
  ZNF676 MUTATED    2  2
  ZNF676 WILD-TYPE  7 11
  ZNF676 MUTATED ZNF676 WILD-TYPE 
               4               18 
  ZNF676 MUTATED ZNF676 WILD-TYPE 
               2               11 
$`ZNF676 MUTATED`
TCGA-DA-A1HV TCGA-EE-A29V TCGA-EE-A2A1 TCGA-ER-A19D 
       48.79         2.43        25.28         3.52 

$`ZNF676 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
        8.09        23.90         9.67        42.84        16.21        15.39 

  ZNF676 MUTATED ZNF676 WILD-TYPE 
            2.43             1.08 
  ZNF676 MUTATED ZNF676 WILD-TYPE 
           48.79            42.84 
  ZNF676 MUTATED ZNF676 WILD-TYPE 
           14.40             9.83 
[1] "2.4 - 48.8 (14.4)" "1.1 - 42.8 (9.8)" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "ZNF676 MUTATED" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"ZNF676 WILD-TYPE"   "ZNF676 MUTATED" "ZNF676 WILD-TYPE"   "ZNF676 MUTATED" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE"   "ZNF676 MUTATED" "ZNF676 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "ZNF676 MUTATED" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"ZNF676 WILD-TYPE"   "ZNF676 MUTATED" "ZNF676 WILD-TYPE"   "ZNF676 MUTATED" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE"   "ZNF676 MUTATED" "ZNF676 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "ZNF676 MUTATED" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"ZNF676 WILD-TYPE"   "ZNF676 MUTATED" "ZNF676 WILD-TYPE"   "ZNF676 MUTATED" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE"   "ZNF676 MUTATED" "ZNF676 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"ZNF676 WILD-TYPE" "ZNF676 WILD-TYPE" 
[1] "hr=" "1.2"
D16V2, continuous
                  vv
clus               DISTANT METASTASIS
  ZNF676 MUTATED                    3
  ZNF676 WILD-TYPE                  5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ZNF676 MUTATED                                                                                          2
  ZNF676 WILD-TYPE                                                                                        7
                  vv
clus               REGIONAL LYMPH NODE
  ZNF676 MUTATED                     5
  ZNF676 WILD-TYPE                  23
D16V3, multiclass
                                                                                          clus
vv                                                                                         ZNF676 MUTATED
  DISTANT METASTASIS                                                                                    3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              2
  REGIONAL LYMPH NODE                                                                                   5
                                                                                          clus
vv                                                                                         ZNF676 WILD-TYPE
  DISTANT METASTASIS                                                                                      5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                7
  REGIONAL LYMPH NODE                                                                                    23
D16V4, binary
                  cls
clus                0  1
  ZNF676 MUTATED    4  6
  ZNF676 WILD-TYPE 12 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF676 MUTATED      4    6
  ZNF676 WILD-TYPE   12   23
        clus
vv       ZNF676 MUTATED ZNF676 WILD-TYPE
  FEMALE              4               12
  MALE                6               23
                  vv
clus               N0 N1A N1B N2A N2B N3
  ZNF676 MUTATED    6   0   1   0   1  0
  ZNF676 WILD-TYPE 21   3   3   1   1  5
D16V5, multiclass
D16V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ZNF676 MUTATED             1       1        0        2        1         0
  ZNF676 WILD-TYPE           0       2        4        4        3         3
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ZNF676 MUTATED           0         1         0          0          1
  ZNF676 WILD-TYPE         4         1         1          1          5
                  vv
clus               STAGE IIIC STAGE IV
  ZNF676 MUTATED            1        0
  ZNF676 WILD-TYPE          5        1
D16V7, multiclass

Clustering(17) Variable = LIPI MUTATION ANALYSIS
D17V1, survival
                sevent
clus2             0  1
  LIPI MUTATED    2  1
  LIPI WILD-TYPE  7 12
  LIPI MUTATED LIPI WILD-TYPE 
             3             19 
  LIPI MUTATED LIPI WILD-TYPE 
             1             12 
$`LIPI MUTATED`
TCGA-DA-A1HV TCGA-EE-A29V TCGA-EE-A2A1 
       48.79         2.43        25.28 

$`LIPI WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
        8.09        23.90         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  LIPI MUTATED LIPI WILD-TYPE 
          2.43           1.08 
  LIPI MUTATED LIPI WILD-TYPE 
         48.79          42.84 
  LIPI MUTATED LIPI WILD-TYPE 
         25.28           9.67 
[1] "2.4 - 48.8 (25.3)" "1.1 - 42.8 (9.7)" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "LIPI MUTATED" "LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"LIPI WILD-TYPE"   "LIPI MUTATED" "LIPI WILD-TYPE"   "LIPI MUTATED" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"LIPI WILD-TYPE" "LIPI WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "LIPI MUTATED" "LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"LIPI WILD-TYPE"   "LIPI MUTATED" "LIPI WILD-TYPE"   "LIPI MUTATED" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"LIPI WILD-TYPE" "LIPI WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "LIPI MUTATED" "LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"LIPI WILD-TYPE"   "LIPI MUTATED" "LIPI WILD-TYPE"   "LIPI MUTATED" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" "LIPI WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"LIPI WILD-TYPE" "LIPI WILD-TYPE" 
[1] "hr=" "2.5"
D17V2, continuous
                vv
clus             DISTANT METASTASIS
  LIPI MUTATED                    1
  LIPI WILD-TYPE                  7
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  LIPI MUTATED                                                                                          1
  LIPI WILD-TYPE                                                                                        8
                vv
clus             REGIONAL LYMPH NODE
  LIPI MUTATED                     5
  LIPI WILD-TYPE                  23
D17V3, multiclass
                                                                                          clus
vv                                                                                         LIPI MUTATED
  DISTANT METASTASIS                                                                                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            1
  REGIONAL LYMPH NODE                                                                                 5
                                                                                          clus
vv                                                                                         LIPI WILD-TYPE
  DISTANT METASTASIS                                                                                    7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              8
  REGIONAL LYMPH NODE                                                                                  23
D17V4, binary
                cls
clus              0  1
  LIPI MUTATED    1  6
  LIPI WILD-TYPE 15 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPI MUTATED      1    6
  LIPI WILD-TYPE   15   23
        clus
vv       LIPI MUTATED LIPI WILD-TYPE
  FEMALE            1             15
  MALE              6             23
                vv
clus             N0 N1A N1B N2A N2B N3
  LIPI MUTATED    3   1   1   0   1  0
  LIPI WILD-TYPE 24   2   3   1   1  5
D17V5, multiclass
D17V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  LIPI MUTATED             0       0        0        1        1         1
  LIPI WILD-TYPE           1       3        4        5        3         2
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  LIPI MUTATED           0         0         0          0          2          1
  LIPI WILD-TYPE         4         2         1          1          4          5
                vv
clus             STAGE IV
  LIPI MUTATED          0
  LIPI WILD-TYPE        1
D17V7, multiclass

Clustering(18) Variable = CADM2 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2              0  1
  CADM2 MUTATED    2  1
  CADM2 WILD-TYPE  7 12
  CADM2 MUTATED CADM2 WILD-TYPE 
              3              19 
  CADM2 MUTATED CADM2 WILD-TYPE 
              1              12 
$`CADM2 MUTATED`
TCGA-D3-A3MV TCGA-EE-A2A2 TCGA-GN-A268 
        5.39        23.90        15.39 

$`CADM2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        2.43         8.09        25.28         9.67         3.52        42.84 
TCGA-GN-A267 
       16.21 

  CADM2 MUTATED CADM2 WILD-TYPE 
           5.39            1.08 
  CADM2 MUTATED CADM2 WILD-TYPE 
          23.90           48.79 
  CADM2 MUTATED CADM2 WILD-TYPE 
          15.39            9.67 
[1] "5.4 - 23.9 (15.4)" "1.1 - 48.8 (9.7)" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE"   "CADM2 MUTATED" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "CADM2 MUTATED" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"CADM2 WILD-TYPE"   "CADM2 MUTATED" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE"   "CADM2 MUTATED" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "CADM2 MUTATED" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"CADM2 WILD-TYPE"   "CADM2 MUTATED" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE"   "CADM2 MUTATED" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "CADM2 MUTATED" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" "CADM2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"CADM2 WILD-TYPE"   "CADM2 MUTATED" 
[1] "hr=" "2"  
D18V2, continuous
                 vv
clus              DISTANT METASTASIS
  CADM2 MUTATED                    1
  CADM2 WILD-TYPE                  7
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CADM2 MUTATED                                                                                          2
  CADM2 WILD-TYPE                                                                                        7
                 vv
clus              REGIONAL LYMPH NODE
  CADM2 MUTATED                     2
  CADM2 WILD-TYPE                  26
D18V3, multiclass
                                                                                          clus
vv                                                                                         CADM2 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  2
                                                                                          clus
vv                                                                                         CADM2 WILD-TYPE
  DISTANT METASTASIS                                                                                     7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   26
D18V4, binary
                 cls
clus               0  1
  CADM2 MUTATED    3  2
  CADM2 WILD-TYPE 13 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CADM2 MUTATED      3    2
  CADM2 WILD-TYPE   13   27
        clus
vv       CADM2 MUTATED CADM2 WILD-TYPE
  FEMALE             3              13
  MALE               2              27
                 vv
clus              N0 N1A N1B N2A N2B N3
  CADM2 MUTATED    3   0   1   1   0  0
  CADM2 WILD-TYPE 24   3   3   0   2  5
D18V5, multiclass
D18V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CADM2 MUTATED             0       0        0        0        0         0
  CADM2 WILD-TYPE           1       3        4        6        4         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CADM2 MUTATED           1         2         0          0          2
  CADM2 WILD-TYPE         3         0         1          1          4
                 vv
clus              STAGE IIIC STAGE IV
  CADM2 MUTATED            0        0
  CADM2 WILD-TYPE          6        1
D18V7, multiclass

Clustering(19) Variable = CDH9 MUTATION ANALYSIS
D19V1, survival
                sevent
clus2             0  1
  CDH9 MUTATED    1  3
  CDH9 WILD-TYPE  8 10
  CDH9 MUTATED CDH9 WILD-TYPE 
             4             18 
  CDH9 MUTATED CDH9 WILD-TYPE 
             3             10 
$`CDH9 MUTATED`
TCGA-EE-A17X TCGA-EE-A29L TCGA-ER-A19N TCGA-GN-A268 
       11.57         1.08        42.84        15.39 

$`CDH9 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        7.00         4.27         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A267 
        8.09        25.28        23.90         9.67         3.52        16.21 

  CDH9 MUTATED CDH9 WILD-TYPE 
          1.08           2.43 
  CDH9 MUTATED CDH9 WILD-TYPE 
         42.84          48.79 
  CDH9 MUTATED CDH9 WILD-TYPE 
        13.480          9.255 
[1] "1.1 - 42.8 (13.5)" "2.4 - 48.8 (9.3)" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE"   "CDH9 MUTATED" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"CDH9 WILD-TYPE"   "CDH9 MUTATED" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE"   "CDH9 MUTATED" 
    TCGA-GN-A267     TCGA-GN-A268 
"CDH9 WILD-TYPE"   "CDH9 MUTATED" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE"   "CDH9 MUTATED" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"CDH9 WILD-TYPE"   "CDH9 MUTATED" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE"   "CDH9 MUTATED" 
    TCGA-GN-A267     TCGA-GN-A268 
"CDH9 WILD-TYPE"   "CDH9 MUTATED" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE"   "CDH9 MUTATED" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"CDH9 WILD-TYPE"   "CDH9 MUTATED" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"CDH9 WILD-TYPE" "CDH9 WILD-TYPE" "CDH9 WILD-TYPE"   "CDH9 MUTATED" 
    TCGA-GN-A267     TCGA-GN-A268 
"CDH9 WILD-TYPE"   "CDH9 MUTATED" 
[1] "hr=" "1.3"
D19V2, continuous
                vv
clus             DISTANT METASTASIS
  CDH9 MUTATED                    2
  CDH9 WILD-TYPE                  6
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CDH9 MUTATED                                                                                          0
  CDH9 WILD-TYPE                                                                                        9
                vv
clus             REGIONAL LYMPH NODE
  CDH9 MUTATED                     7
  CDH9 WILD-TYPE                  21
D19V3, multiclass
                                                                                          clus
vv                                                                                         CDH9 MUTATED
  DISTANT METASTASIS                                                                                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            0
  REGIONAL LYMPH NODE                                                                                 7
                                                                                          clus
vv                                                                                         CDH9 WILD-TYPE
  DISTANT METASTASIS                                                                                    6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              9
  REGIONAL LYMPH NODE                                                                                  21
D19V4, binary
                cls
clus              0  1
  CDH9 MUTATED    4  5
  CDH9 WILD-TYPE 12 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH9 MUTATED      4    5
  CDH9 WILD-TYPE   12   24
        clus
vv       CDH9 MUTATED CDH9 WILD-TYPE
  FEMALE            4             12
  MALE              5             24
                vv
clus             N0 N1A N1B N2A N2B N3
  CDH9 MUTATED    7   0   0   0   0  1
  CDH9 WILD-TYPE 20   3   4   1   2  4
D19V5, multiclass
D19V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CDH9 MUTATED             0       1        3        0        1         1
  CDH9 WILD-TYPE           1       2        1        6        3         2
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CDH9 MUTATED           1         0         0          0          0          1
  CDH9 WILD-TYPE         3         2         1          1          6          5
                vv
clus             STAGE IV
  CDH9 MUTATED          0
  CDH9 WILD-TYPE        1
D19V7, multiclass

Clustering(20) Variable = OR52E2 MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2               0  1
  OR52E2 MUTATED    1  1
  OR52E2 WILD-TYPE  8 12
  OR52E2 MUTATED OR52E2 WILD-TYPE 
               2               20 
  OR52E2 MUTATED OR52E2 WILD-TYPE 
               1               12 
$`OR52E2 MUTATED`
TCGA-EE-A29L TCGA-ER-A19N 
        1.08        42.84 

$`OR52E2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        7.00        11.57         4.27         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        2.43         8.09        25.28        23.90         9.67         3.52 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  OR52E2 MUTATED OR52E2 WILD-TYPE 
            1.08             2.43 
  OR52E2 MUTATED OR52E2 WILD-TYPE 
           42.84            48.79 
  OR52E2 MUTATED OR52E2 WILD-TYPE 
           21.96             9.83 
[1] "1.1 - 42.8 (22.0)" "2.4 - 48.8 (9.8)" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"OR52E2 WILD-TYPE"   "OR52E2 MUTATED" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE"   "OR52E2 MUTATED" 
      TCGA-GN-A267       TCGA-GN-A268 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"OR52E2 WILD-TYPE"   "OR52E2 MUTATED" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE"   "OR52E2 MUTATED" 
      TCGA-GN-A267       TCGA-GN-A268 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"OR52E2 WILD-TYPE"   "OR52E2 MUTATED" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE"   "OR52E2 MUTATED" 
      TCGA-GN-A267       TCGA-GN-A268 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
[1] "Remove cluster labels:" "OR52E2 MUTATED"        
clus
  OR52E2 MUTATED OR52E2 WILD-TYPE 
               2               20 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29Q       TCGA-EE-A29R       TCGA-EE-A29S 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1       TCGA-EE-A2A2 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
      TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-GN-A267       TCGA-GN-A268 
"OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" "OR52E2 WILD-TYPE" 
D20V2, continuous
                  vv
clus               DISTANT METASTASIS
  OR52E2 MUTATED                    1
  OR52E2 WILD-TYPE                  7
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  OR52E2 MUTATED                                                                                          0
  OR52E2 WILD-TYPE                                                                                        9
                  vv
clus               REGIONAL LYMPH NODE
  OR52E2 MUTATED                     5
  OR52E2 WILD-TYPE                  23
D20V3, multiclass
                                                                                          clus
vv                                                                                         OR52E2 MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              0
  REGIONAL LYMPH NODE                                                                                   5
                                                                                          clus
vv                                                                                         OR52E2 WILD-TYPE
  DISTANT METASTASIS                                                                                      7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                9
  REGIONAL LYMPH NODE                                                                                    23
D20V4, binary
                  cls
clus                0  1
  OR52E2 MUTATED    2  4
  OR52E2 WILD-TYPE 14 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52E2 MUTATED      2    4
  OR52E2 WILD-TYPE   14   25
        clus
vv       OR52E2 MUTATED OR52E2 WILD-TYPE
  FEMALE              2               14
  MALE                4               25
                  vv
clus               N0 N1A N1B N2A N2B N3
  OR52E2 MUTATED    4   0   0   0   0  1
  OR52E2 WILD-TYPE 23   3   4   1   2  4
D20V5, multiclass
D20V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  OR52E2 MUTATED             0       1        2        0        1         0
  OR52E2 WILD-TYPE           1       2        2        6        3         3
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  OR52E2 MUTATED           0         0         0          0          0
  OR52E2 WILD-TYPE         4         2         1          1          6
                  vv
clus               STAGE IIIC STAGE IV
  OR52E2 MUTATED            1        0
  OR52E2 WILD-TYPE          5        1
D20V7, multiclass

Clustering(21) Variable = CLEC5A MUTATION ANALYSIS
D21V1, survival
                  sevent
clus2               0  1
  CLEC5A MUTATED    1  1
  CLEC5A WILD-TYPE  8 12
  CLEC5A MUTATED CLEC5A WILD-TYPE 
               2               20 
  CLEC5A MUTATED CLEC5A WILD-TYPE 
               1               12 
$`CLEC5A MUTATED`
TCGA-EE-A29S TCGA-EE-A29V 
        9.99         2.43 

$`CLEC5A WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
        7.00        11.57         4.27         1.08         8.12         8.84 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  CLEC5A MUTATED CLEC5A WILD-TYPE 
            2.43             1.08 
  CLEC5A MUTATED CLEC5A WILD-TYPE 
            9.99            48.79 
  CLEC5A MUTATED CLEC5A WILD-TYPE 
            6.21            10.62 
[1] "2.4 - 10.0 (6.2)"  "1.1 - 48.8 (10.6)"
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "CLEC5A MUTATED"   "CLEC5A MUTATED" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "CLEC5A MUTATED"   "CLEC5A MUTATED" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "CLEC5A MUTATED"   "CLEC5A MUTATED" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
[1] "Remove cluster labels:" "CLEC5A MUTATED"        
clus
  CLEC5A MUTATED CLEC5A WILD-TYPE 
               2               20 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-EE-A29X       TCGA-EE-A2A1       TCGA-EE-A2A2       TCGA-EE-A2A5 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
      TCGA-ER-A19D       TCGA-ER-A19N       TCGA-GN-A267       TCGA-GN-A268 
"CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" "CLEC5A WILD-TYPE" 
D21V2, continuous
                  vv
clus               DISTANT METASTASIS
  CLEC5A MUTATED                    2
  CLEC5A WILD-TYPE                  6
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CLEC5A MUTATED                                                                                          0
  CLEC5A WILD-TYPE                                                                                        9
                  vv
clus               REGIONAL LYMPH NODE
  CLEC5A MUTATED                     2
  CLEC5A WILD-TYPE                  26
D21V3, multiclass
                                                                                          clus
vv                                                                                         CLEC5A MUTATED
  DISTANT METASTASIS                                                                                    2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              0
  REGIONAL LYMPH NODE                                                                                   2
                                                                                          clus
vv                                                                                         CLEC5A WILD-TYPE
  DISTANT METASTASIS                                                                                      6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                9
  REGIONAL LYMPH NODE                                                                                    26
D21V4, binary
                  cls
clus                0  1
  CLEC5A MUTATED    0  4
  CLEC5A WILD-TYPE 16 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC5A MUTATED      0    4
  CLEC5A WILD-TYPE   16   25
        clus
vv       CLEC5A MUTATED CLEC5A WILD-TYPE
  FEMALE              0               16
  MALE                4               25
                  vv
clus               N0 N1A N1B N2A N2B N3
  CLEC5A MUTATED    3   0   1   0   0  0
  CLEC5A WILD-TYPE 24   3   3   1   2  5
D21V5, multiclass
D21V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CLEC5A MUTATED             1       1        0        0        0         1
  CLEC5A WILD-TYPE           0       2        4        6        4         2
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CLEC5A MUTATED           0         0         0          0          0
  CLEC5A WILD-TYPE         4         2         1          1          6
                  vv
clus               STAGE IIIC STAGE IV
  CLEC5A MUTATED            1        0
  CLEC5A WILD-TYPE          5        1
D21V7, multiclass

Clustering(22) Variable = HIST1H2AA MUTATION ANALYSIS
D22V1, survival
                     sevent
clus2                  0  1
  HIST1H2AA WILD-TYPE  9 13
HIST1H2AA WILD-TYPE 
                 22 
[1] 13
$`HIST1H2AA WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
        7.00        11.57         4.27         1.08         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        9.99         2.43         8.09        25.28        23.90         9.67 
TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
        3.52        42.84        16.21        15.39 

HIST1H2AA WILD-TYPE 
               1.08 
HIST1H2AA WILD-TYPE 
              48.79 
HIST1H2AA WILD-TYPE 
               9.83 
[1] "1.1 - 48.8 (9.8)"
         TCGA-D3-A1Q1          TCGA-D3-A1Q8          TCGA-D3-A2J8 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-D3-A3MV          TCGA-DA-A1HV          TCGA-DA-A1I1 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-DA-A3F3          TCGA-EE-A17X          TCGA-EE-A185 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-EE-A29L          TCGA-EE-A29Q          TCGA-EE-A29R 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-EE-A29S          TCGA-EE-A29V          TCGA-EE-A29X 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-EE-A2A1          TCGA-EE-A2A2          TCGA-EE-A2A5 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-ER-A19D          TCGA-ER-A19N          TCGA-GN-A267 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-GN-A268 
"HIST1H2AA WILD-TYPE" 
         TCGA-D3-A1Q1          TCGA-D3-A1Q8          TCGA-D3-A2J8 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-D3-A3MV          TCGA-DA-A1HV          TCGA-DA-A1I1 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-DA-A3F3          TCGA-EE-A17X          TCGA-EE-A185 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-EE-A29L          TCGA-EE-A29Q          TCGA-EE-A29R 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-EE-A29S          TCGA-EE-A29V          TCGA-EE-A29X 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-EE-A2A1          TCGA-EE-A2A2          TCGA-EE-A2A5 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-ER-A19D          TCGA-ER-A19N          TCGA-GN-A267 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-GN-A268 
"HIST1H2AA WILD-TYPE" 
         TCGA-D3-A1Q1          TCGA-D3-A1Q8          TCGA-D3-A2J8 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-D3-A3MV          TCGA-DA-A1HV          TCGA-DA-A1I1 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-DA-A3F3          TCGA-EE-A17X          TCGA-EE-A185 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-EE-A29L          TCGA-EE-A29Q          TCGA-EE-A29R 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-EE-A29S          TCGA-EE-A29V          TCGA-EE-A29X 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-EE-A2A1          TCGA-EE-A2A2          TCGA-EE-A2A5 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-ER-A19D          TCGA-ER-A19N          TCGA-GN-A267 
"HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" "HIST1H2AA WILD-TYPE" 
         TCGA-GN-A268 
"HIST1H2AA WILD-TYPE" 
D22V2, continuous
                     vv
clus                  DISTANT METASTASIS
  HIST1H2AA MUTATED                    0
  HIST1H2AA WILD-TYPE                  8
                     vv
clus                  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  HIST1H2AA MUTATED                                                                                          0
  HIST1H2AA WILD-TYPE                                                                                        9
                     vv
clus                  REGIONAL LYMPH NODE
  HIST1H2AA MUTATED                     3
  HIST1H2AA WILD-TYPE                  25
D22V3, multiclass
                                                                                          clus
vv                                                                                         HIST1H2AA MUTATED
  DISTANT METASTASIS                                                                                       0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 0
  REGIONAL LYMPH NODE                                                                                      3
                                                                                          clus
vv                                                                                         HIST1H2AA WILD-TYPE
  DISTANT METASTASIS                                                                                         8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                   9
  REGIONAL LYMPH NODE                                                                                       25
D22V4, binary
                     cls
clus                   0  1
  HIST1H2AA MUTATED    1  2
  HIST1H2AA WILD-TYPE 15 27
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2AA MUTATED      1    2
  HIST1H2AA WILD-TYPE   15   27
        clus
vv       HIST1H2AA MUTATED HIST1H2AA WILD-TYPE
  FEMALE                 1                  15
  MALE                   2                  27
                     vv
clus                  N0 N1A N1B N2A N2B N3
  HIST1H2AA MUTATED    3   0   0   0   0  0
  HIST1H2AA WILD-TYPE 24   3   4   1   2  5
D22V5, multiclass
D22V6, continuous
                     vv
clus                  I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  HIST1H2AA MUTATED             0       1        1        1        0         0
  HIST1H2AA WILD-TYPE           1       2        3        5        4         3
                     vv
clus                  STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  HIST1H2AA MUTATED           0         0         0          0          0
  HIST1H2AA WILD-TYPE         4         2         1          1          6
                     vv
clus                  STAGE IIIC STAGE IV
  HIST1H2AA MUTATED            0        0
  HIST1H2AA WILD-TYPE          6        1
D22V7, multiclass

Clustering(23) Variable = KIAA1257 MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  KIAA1257 MUTATED    0  1
  KIAA1257 WILD-TYPE  9 12
  KIAA1257 MUTATED KIAA1257 WILD-TYPE 
                 1                 21 
  KIAA1257 MUTATED KIAA1257 WILD-TYPE 
                 1                 12 
$`KIAA1257 MUTATED`
TCGA-EE-A29L 
        1.08 

$`KIAA1257 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        7.00        11.57         4.27         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        2.43         8.09        25.28        23.90         9.67         3.52 
TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       42.84        16.21        15.39 

  KIAA1257 MUTATED KIAA1257 WILD-TYPE 
              1.08               2.43 
  KIAA1257 MUTATED KIAA1257 WILD-TYPE 
              1.08              48.79 
  KIAA1257 MUTATED KIAA1257 WILD-TYPE 
              1.08               9.99 
[1] "1.1 - 1.1 (1.1)"   "2.4 - 48.8 (10.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "KIAA1257 MUTATED" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-GN-A268 
"KIAA1257 WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "KIAA1257 MUTATED" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-GN-A268 
"KIAA1257 WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "KIAA1257 MUTATED" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-GN-A268 
"KIAA1257 WILD-TYPE" 
[1] "Remove cluster labels:" "KIAA1257 MUTATED"      
clus
  KIAA1257 MUTATED KIAA1257 WILD-TYPE 
                 1                 21 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A1 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-ER-A19D 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
        TCGA-ER-A19N         TCGA-GN-A267         TCGA-GN-A268 
"KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" "KIAA1257 WILD-TYPE" 
D23V2, continuous
                    vv
clus                 DISTANT METASTASIS
  KIAA1257 MUTATED                    2
  KIAA1257 WILD-TYPE                  6
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  KIAA1257 MUTATED                                                                                          1
  KIAA1257 WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  KIAA1257 MUTATED                     1
  KIAA1257 WILD-TYPE                  27
D23V3, multiclass
                                                                                          clus
vv                                                                                         KIAA1257 MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     1
                                                                                          clus
vv                                                                                         KIAA1257 WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      27
D23V4, binary
                    cls
clus                  0  1
  KIAA1257 MUTATED    1  3
  KIAA1257 WILD-TYPE 15 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1257 MUTATED      1    3
  KIAA1257 WILD-TYPE   15   26
        clus
vv       KIAA1257 MUTATED KIAA1257 WILD-TYPE
  FEMALE                1                 15
  MALE                  3                 26
                    vv
clus                 N0 N1A N1B N2A N2B N3
  KIAA1257 MUTATED    1   1   0   0   0  1
  KIAA1257 WILD-TYPE 26   2   4   1   2  4
D23V5, multiclass
D23V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  KIAA1257 MUTATED             1       0        0        0        0         0
  KIAA1257 WILD-TYPE           0       3        4        6        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  KIAA1257 MUTATED           0         0         0          0          1
  KIAA1257 WILD-TYPE         4         2         1          1          5
                    vv
clus                 STAGE IIIC STAGE IV
  KIAA1257 MUTATED            1        0
  KIAA1257 WILD-TYPE          5        1
D23V7, multiclass

Clustering(24) Variable = PCDH18 MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2               0  1
  PCDH18 MUTATED    3  3
  PCDH18 WILD-TYPE  6 10
  PCDH18 MUTATED PCDH18 WILD-TYPE 
               6               16 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
               3               10 
$`PCDH18 MUTATED`
TCGA-EE-A29L TCGA-EE-A29S TCGA-EE-A2A1 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A268 
        1.08         9.99        25.28         3.52        42.84        15.39 

$`PCDH18 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
        7.00        11.57         4.27         8.12         8.84         2.43 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-GN-A267 
        8.09        23.90         9.67        16.21 

  PCDH18 MUTATED PCDH18 WILD-TYPE 
            1.08             2.43 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
           42.84            48.79 
  PCDH18 MUTATED PCDH18 WILD-TYPE 
          12.690            9.255 
[1] "1.1 - 42.8 (12.7)" "2.4 - 48.8 (9.3)" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"PCDH18 WILD-TYPE"   "PCDH18 MUTATED" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "PCDH18 MUTATED" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE"   "PCDH18 MUTATED" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE"   "PCDH18 MUTATED"   "PCDH18 MUTATED" 
      TCGA-GN-A267       TCGA-GN-A268 
"PCDH18 WILD-TYPE"   "PCDH18 MUTATED" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"PCDH18 WILD-TYPE"   "PCDH18 MUTATED" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "PCDH18 MUTATED" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE"   "PCDH18 MUTATED" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE"   "PCDH18 MUTATED"   "PCDH18 MUTATED" 
      TCGA-GN-A267       TCGA-GN-A268 
"PCDH18 WILD-TYPE"   "PCDH18 MUTATED" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"PCDH18 WILD-TYPE"   "PCDH18 MUTATED" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "PCDH18 MUTATED" "PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE"   "PCDH18 MUTATED" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"PCDH18 WILD-TYPE" "PCDH18 WILD-TYPE"   "PCDH18 MUTATED"   "PCDH18 MUTATED" 
      TCGA-GN-A267       TCGA-GN-A268 
"PCDH18 WILD-TYPE"   "PCDH18 MUTATED" 
[1] "hr=" "1.2"
D24V2, continuous
                  vv
clus               DISTANT METASTASIS
  PCDH18 MUTATED                    1
  PCDH18 WILD-TYPE                  7
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  PCDH18 MUTATED                                                                                          1
  PCDH18 WILD-TYPE                                                                                        8
                  vv
clus               REGIONAL LYMPH NODE
  PCDH18 MUTATED                     7
  PCDH18 WILD-TYPE                  21
D24V3, multiclass
                                                                                          clus
vv                                                                                         PCDH18 MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   7
                                                                                          clus
vv                                                                                         PCDH18 WILD-TYPE
  DISTANT METASTASIS                                                                                      7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    21
D24V4, binary
                  cls
clus                0  1
  PCDH18 MUTATED    3  6
  PCDH18 WILD-TYPE 13 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH18 MUTATED      3    6
  PCDH18 WILD-TYPE   13   23
        clus
vv       PCDH18 MUTATED PCDH18 WILD-TYPE
  FEMALE              3               13
  MALE                6               23
                  vv
clus               N0 N1A N1B N2A N2B N3
  PCDH18 MUTATED    6   1   0   0   0  1
  PCDH18 WILD-TYPE 21   2   4   1   2  4
D24V5, multiclass
D24V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  PCDH18 MUTATED             0       0        1        2        1         1
  PCDH18 WILD-TYPE           1       3        3        4        3         2
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  PCDH18 MUTATED           1         0         0          0          1
  PCDH18 WILD-TYPE         3         2         1          1          5
                  vv
clus               STAGE IIIC STAGE IV
  PCDH18 MUTATED            1        0
  PCDH18 WILD-TYPE          5        1
D24V7, multiclass

Clustering(25) Variable = SPOCK3 MUTATION ANALYSIS
D25V1, survival
                  sevent
clus2               0  1
  SPOCK3 MUTATED    1  1
  SPOCK3 WILD-TYPE  8 12
  SPOCK3 MUTATED SPOCK3 WILD-TYPE 
               2               20 
  SPOCK3 MUTATED SPOCK3 WILD-TYPE 
               1               12 
$`SPOCK3 MUTATED`
TCGA-EE-A17X TCGA-EE-A29S 
       11.57         9.99 

$`SPOCK3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
        7.00         4.27         1.08         8.12         8.84         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  SPOCK3 MUTATED SPOCK3 WILD-TYPE 
            9.99             1.08 
  SPOCK3 MUTATED SPOCK3 WILD-TYPE 
           11.57            48.79 
  SPOCK3 MUTATED SPOCK3 WILD-TYPE 
          10.780            9.255 
[1] "10.0 - 11.6 (10.8)" "1.1 - 48.8 (9.3)"  
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE"   "SPOCK3 MUTATED" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "SPOCK3 MUTATED" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE"   "SPOCK3 MUTATED" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "SPOCK3 MUTATED" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE"   "SPOCK3 MUTATED" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "SPOCK3 MUTATED" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
[1] "Remove cluster labels:" "SPOCK3 MUTATED"        
clus
  SPOCK3 MUTATED SPOCK3 WILD-TYPE 
               2               20 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A185 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R       TCGA-EE-A29V 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-EE-A29X       TCGA-EE-A2A1       TCGA-EE-A2A2       TCGA-EE-A2A5 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
      TCGA-ER-A19D       TCGA-ER-A19N       TCGA-GN-A267       TCGA-GN-A268 
"SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" "SPOCK3 WILD-TYPE" 
D25V2, continuous
                  vv
clus               DISTANT METASTASIS
  SPOCK3 MUTATED                    0
  SPOCK3 WILD-TYPE                  8
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  SPOCK3 MUTATED                                                                                          0
  SPOCK3 WILD-TYPE                                                                                        9
                  vv
clus               REGIONAL LYMPH NODE
  SPOCK3 MUTATED                     6
  SPOCK3 WILD-TYPE                  22
D25V3, multiclass
                                                                                          clus
vv                                                                                         SPOCK3 MUTATED
  DISTANT METASTASIS                                                                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              0
  REGIONAL LYMPH NODE                                                                                   6
                                                                                          clus
vv                                                                                         SPOCK3 WILD-TYPE
  DISTANT METASTASIS                                                                                      8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                9
  REGIONAL LYMPH NODE                                                                                    22
D25V4, binary
                  cls
clus                0  1
  SPOCK3 MUTATED    0  6
  SPOCK3 WILD-TYPE 16 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPOCK3 MUTATED      0    6
  SPOCK3 WILD-TYPE   16   23
        clus
vv       SPOCK3 MUTATED SPOCK3 WILD-TYPE
  FEMALE              0               16
  MALE                6               23
                  vv
clus               N0 N1A N1B N2A N2B N3
  SPOCK3 MUTATED    6   0   0   0   0  0
  SPOCK3 WILD-TYPE 21   3   4   1   2  5
D25V5, multiclass
D25V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  SPOCK3 MUTATED             0       1        1        0        3         1
  SPOCK3 WILD-TYPE           1       2        3        6        1         2
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  SPOCK3 MUTATED           0         0         0          0          0
  SPOCK3 WILD-TYPE         4         2         1          1          6
                  vv
clus               STAGE IIIC STAGE IV
  SPOCK3 MUTATED            0        0
  SPOCK3 WILD-TYPE          6        1
D25V7, multiclass

Clustering(26) Variable = OR2G6 MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2              0  1
  OR2G6 MUTATED    4  2
  OR2G6 WILD-TYPE  5 11
  OR2G6 MUTATED OR2G6 WILD-TYPE 
              6              16 
  OR2G6 MUTATED OR2G6 WILD-TYPE 
              2              11 
$`OR2G6 MUTATED`
TCGA-DA-A1HV TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A2A2 TCGA-EE-A2A5 
       48.79         1.08         8.12         9.99        23.90         9.67 

$`OR2G6 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
       11.57         4.27         8.84         2.43         8.09        25.28 
TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
        3.52        42.84        16.21        15.39 

  OR2G6 MUTATED OR2G6 WILD-TYPE 
           1.08            2.43 
  OR2G6 MUTATED OR2G6 WILD-TYPE 
          48.79           42.84 
  OR2G6 MUTATED OR2G6 WILD-TYPE 
          9.830          10.205 
[1] "1.1 - 48.8 (9.8)"  "2.4 - 42.8 (10.2)"
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "OR2G6 MUTATED" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"OR2G6 WILD-TYPE"   "OR2G6 MUTATED"   "OR2G6 MUTATED" "OR2G6 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "OR2G6 MUTATED" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "OR2G6 MUTATED"   "OR2G6 MUTATED" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "OR2G6 MUTATED" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"OR2G6 WILD-TYPE"   "OR2G6 MUTATED"   "OR2G6 MUTATED" "OR2G6 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "OR2G6 MUTATED" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "OR2G6 MUTATED"   "OR2G6 MUTATED" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "OR2G6 MUTATED" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"OR2G6 WILD-TYPE"   "OR2G6 MUTATED"   "OR2G6 MUTATED" "OR2G6 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "OR2G6 MUTATED" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "OR2G6 MUTATED"   "OR2G6 MUTATED" "OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"OR2G6 WILD-TYPE" "OR2G6 WILD-TYPE" 
[1] "hr=" "2"  
D26V2, continuous
                 vv
clus              DISTANT METASTASIS
  OR2G6 MUTATED                    0
  OR2G6 WILD-TYPE                  8
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  OR2G6 MUTATED                                                                                          3
  OR2G6 WILD-TYPE                                                                                        6
                 vv
clus              REGIONAL LYMPH NODE
  OR2G6 MUTATED                     5
  OR2G6 WILD-TYPE                  23
D26V3, multiclass
                                                                                          clus
vv                                                                                         OR2G6 MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             3
  REGIONAL LYMPH NODE                                                                                  5
                                                                                          clus
vv                                                                                         OR2G6 WILD-TYPE
  DISTANT METASTASIS                                                                                     8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               6
  REGIONAL LYMPH NODE                                                                                   23
D26V4, binary
                 cls
clus               0  1
  OR2G6 MUTATED    3  5
  OR2G6 WILD-TYPE 13 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2G6 MUTATED      3    5
  OR2G6 WILD-TYPE   13   24
        clus
vv       OR2G6 MUTATED OR2G6 WILD-TYPE
  FEMALE             3              13
  MALE               5              24
                 vv
clus              N0 N1A N1B N2A N2B N3
  OR2G6 MUTATED    5   0   1   0   1  1
  OR2G6 WILD-TYPE 22   3   3   1   1  4
D26V5, multiclass
D26V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  OR2G6 MUTATED             0       0        1        1        0         1
  OR2G6 WILD-TYPE           1       3        3        5        4         2
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  OR2G6 MUTATED           1         1         0          0          2
  OR2G6 WILD-TYPE         3         1         1          1          4
                 vv
clus              STAGE IIIC STAGE IV
  OR2G6 MUTATED            1        0
  OR2G6 WILD-TYPE          5        1
D26V7, multiclass

Clustering(27) Variable = STXBP5L MUTATION ANALYSIS
D27V1, survival
                   sevent
clus2                0  1
  STXBP5L MUTATED    4  1
  STXBP5L WILD-TYPE  5 12
  STXBP5L MUTATED STXBP5L WILD-TYPE 
                5                17 
  STXBP5L MUTATED STXBP5L WILD-TYPE 
                1                12 
$`STXBP5L MUTATED`
TCGA-D3-A3MV TCGA-DA-A1HV TCGA-EE-A29R TCGA-EE-A29S TCGA-ER-A19D 
        5.39        48.79         8.84         9.99         3.52 

$`STXBP5L WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       16.47        28.08         8.38        39.19         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
        4.27         1.08         8.12         2.43         8.09        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       23.90         9.67        42.84        16.21        15.39 

  STXBP5L MUTATED STXBP5L WILD-TYPE 
             3.52              1.08 
  STXBP5L MUTATED STXBP5L WILD-TYPE 
            48.79             42.84 
  STXBP5L MUTATED STXBP5L WILD-TYPE 
             8.84             11.57 
[1] "3.5 - 48.8 (8.8)"  "1.1 - 42.8 (11.6)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE"   "STXBP5L MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "STXBP5L MUTATED" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE"   "STXBP5L MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "STXBP5L MUTATED" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE"   "STXBP5L MUTATED" "STXBP5L WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE"   "STXBP5L MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "STXBP5L MUTATED" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE"   "STXBP5L MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "STXBP5L MUTATED" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE"   "STXBP5L MUTATED" "STXBP5L WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE"   "STXBP5L MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "STXBP5L MUTATED" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE"   "STXBP5L MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "STXBP5L MUTATED" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE"   "STXBP5L MUTATED" "STXBP5L WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"STXBP5L WILD-TYPE" "STXBP5L WILD-TYPE" 
[1] "hr=" "2.7"
D27V2, continuous
                   vv
clus                DISTANT METASTASIS
  STXBP5L MUTATED                    2
  STXBP5L WILD-TYPE                  6
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  STXBP5L MUTATED                                                                                          3
  STXBP5L WILD-TYPE                                                                                        6
                   vv
clus                REGIONAL LYMPH NODE
  STXBP5L MUTATED                     5
  STXBP5L WILD-TYPE                  23
D27V3, multiclass
                                                                                          clus
vv                                                                                         STXBP5L MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         STXBP5L WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 6
  REGIONAL LYMPH NODE                                                                                     23
D27V4, binary
                   cls
clus                 0  1
  STXBP5L MUTATED    6  4
  STXBP5L WILD-TYPE 10 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  STXBP5L MUTATED      6    4
  STXBP5L WILD-TYPE   10   25
        clus
vv       STXBP5L MUTATED STXBP5L WILD-TYPE
  FEMALE               6                10
  MALE                 4                25
                   vv
clus                N0 N1A N1B N2A N2B N3
  STXBP5L MUTATED    5   1   1   1   1  0
  STXBP5L WILD-TYPE 22   2   3   0   1  5
D27V5, multiclass
D27V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  STXBP5L MUTATED             0       1        1        1        1         1
  STXBP5L WILD-TYPE           1       2        3        5        3         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  STXBP5L MUTATED           0         0         0          0          3
  STXBP5L WILD-TYPE         4         2         1          1          3
                   vv
clus                STAGE IIIC STAGE IV
  STXBP5L MUTATED            1        0
  STXBP5L WILD-TYPE          5        1
D27V7, multiclass

Clustering(28) Variable = CNGB3 MUTATION ANALYSIS
D28V1, survival
                 sevent
clus2              0  1
  CNGB3 MUTATED    0  3
  CNGB3 WILD-TYPE  9 10
  CNGB3 MUTATED CNGB3 WILD-TYPE 
              3              19 
  CNGB3 MUTATED CNGB3 WILD-TYPE 
              3              10 
$`CNGB3 MUTATED`
TCGA-D3-A2J8 TCGA-EE-A17X TCGA-EE-A29L 
        8.38        11.57         1.08 

$`CNGB3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         5.39        48.79        39.19         7.00 
TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
        4.27         8.12         8.84         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
       25.28        23.90         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  CNGB3 MUTATED CNGB3 WILD-TYPE 
           1.08            2.43 
  CNGB3 MUTATED CNGB3 WILD-TYPE 
          11.57           48.79 
  CNGB3 MUTATED CNGB3 WILD-TYPE 
           8.38            9.99 
[1] "1.1 - 11.6 (8.4)"  "2.4 - 48.8 (10.0)"
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE"   "CNGB3 MUTATED" "CNGB3 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE"   "CNGB3 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"CNGB3 WILD-TYPE"   "CNGB3 MUTATED" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE"   "CNGB3 MUTATED" "CNGB3 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE"   "CNGB3 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"CNGB3 WILD-TYPE"   "CNGB3 MUTATED" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE"   "CNGB3 MUTATED" "CNGB3 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE"   "CNGB3 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"CNGB3 WILD-TYPE"   "CNGB3 MUTATED" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"CNGB3 WILD-TYPE" "CNGB3 WILD-TYPE" 
[1] "hr=" "4"  
D28V2, continuous
                 vv
clus              DISTANT METASTASIS
  CNGB3 MUTATED                    1
  CNGB3 WILD-TYPE                  7
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CNGB3 MUTATED                                                                                          2
  CNGB3 WILD-TYPE                                                                                        7
                 vv
clus              REGIONAL LYMPH NODE
  CNGB3 MUTATED                     6
  CNGB3 WILD-TYPE                  22
D28V3, multiclass
                                                                                          clus
vv                                                                                         CNGB3 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  6
                                                                                          clus
vv                                                                                         CNGB3 WILD-TYPE
  DISTANT METASTASIS                                                                                     7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   22
D28V4, binary
                 cls
clus               0  1
  CNGB3 MUTATED    0  9
  CNGB3 WILD-TYPE 16 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGB3 MUTATED      0    9
  CNGB3 WILD-TYPE   16   20
        clus
vv       CNGB3 MUTATED CNGB3 WILD-TYPE
  FEMALE             0              16
  MALE               9              20
                 vv
clus              N0 N1A N1B N2A N2B N3
  CNGB3 MUTATED    7   1   0   0   0  1
  CNGB3 WILD-TYPE 20   2   4   1   2  4
D28V5, multiclass
D28V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CNGB3 MUTATED             1       1        2        1        1         1
  CNGB3 WILD-TYPE           0       2        2        5        3         2
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CNGB3 MUTATED           0         0         0          0          1
  CNGB3 WILD-TYPE         4         2         1          1          5
                 vv
clus              STAGE IIIC STAGE IV
  CNGB3 MUTATED            1        0
  CNGB3 WILD-TYPE          5        1
D28V7, multiclass

Clustering(29) Variable = HHIPL2 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2               0  1
  HHIPL2 MUTATED    0  2
  HHIPL2 WILD-TYPE  9 11
  HHIPL2 MUTATED HHIPL2 WILD-TYPE 
               2               20 
  HHIPL2 MUTATED HHIPL2 WILD-TYPE 
               2               11 
$`HHIPL2 MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J8 
       16.47         8.38 

$`HHIPL2 WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       28.08         5.39        48.79        39.19         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        4.27         1.08         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  HHIPL2 MUTATED HHIPL2 WILD-TYPE 
            8.38             1.08 
  HHIPL2 MUTATED HHIPL2 WILD-TYPE 
           16.47            48.79 
  HHIPL2 MUTATED HHIPL2 WILD-TYPE 
          12.425            9.830 
[1] "8.4 - 16.5 (12.4)" "1.1 - 48.8 (9.8)" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
  "HHIPL2 MUTATED" "HHIPL2 WILD-TYPE"   "HHIPL2 MUTATED" "HHIPL2 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
  "HHIPL2 MUTATED" "HHIPL2 WILD-TYPE"   "HHIPL2 MUTATED" "HHIPL2 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
  "HHIPL2 MUTATED" "HHIPL2 WILD-TYPE"   "HHIPL2 MUTATED" "HHIPL2 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
[1] "Remove cluster labels:" "HHIPL2 MUTATED"        
clus
  HHIPL2 MUTATED HHIPL2 WILD-TYPE 
               2               20 
      TCGA-D3-A1Q8       TCGA-D3-A3MV       TCGA-DA-A1HV       TCGA-DA-A1I1 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-DA-A3F3       TCGA-EE-A17X       TCGA-EE-A185       TCGA-EE-A29L 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-EE-A29Q       TCGA-EE-A29R       TCGA-EE-A29S       TCGA-EE-A29V 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-EE-A29X       TCGA-EE-A2A1       TCGA-EE-A2A2       TCGA-EE-A2A5 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
      TCGA-ER-A19D       TCGA-ER-A19N       TCGA-GN-A267       TCGA-GN-A268 
"HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" "HHIPL2 WILD-TYPE" 
D29V2, continuous
                  vv
clus               DISTANT METASTASIS
  HHIPL2 MUTATED                    0
  HHIPL2 WILD-TYPE                  8
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  HHIPL2 MUTATED                                                                                          1
  HHIPL2 WILD-TYPE                                                                                        8
                  vv
clus               REGIONAL LYMPH NODE
  HHIPL2 MUTATED                     2
  HHIPL2 WILD-TYPE                  26
D29V3, multiclass
                                                                                          clus
vv                                                                                         HHIPL2 MUTATED
  DISTANT METASTASIS                                                                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   2
                                                                                          clus
vv                                                                                         HHIPL2 WILD-TYPE
  DISTANT METASTASIS                                                                                      8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    26
D29V4, binary
                  cls
clus                0  1
  HHIPL2 MUTATED    2  1
  HHIPL2 WILD-TYPE 14 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HHIPL2 MUTATED      2    1
  HHIPL2 WILD-TYPE   14   28
        clus
vv       HHIPL2 MUTATED HHIPL2 WILD-TYPE
  FEMALE              2               14
  MALE                1               28
                  vv
clus               N0 N1A N1B N2A N2B N3
  HHIPL2 MUTATED    2   0   0   0   0  1
  HHIPL2 WILD-TYPE 25   3   4   1   2  4
D29V5, multiclass
D29V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  HHIPL2 MUTATED             0       0        0        1        0         0
  HHIPL2 WILD-TYPE           1       3        4        5        4         3
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  HHIPL2 MUTATED           1         0         0          0          0
  HHIPL2 WILD-TYPE         3         2         1          1          6
                  vv
clus               STAGE IIIC STAGE IV
  HHIPL2 MUTATED            1        0
  HHIPL2 WILD-TYPE          5        1
D29V7, multiclass

Clustering(30) Variable = OR10G8 MUTATION ANALYSIS
D30V1, survival
                  sevent
clus2               0  1
  OR10G8 MUTATED    0  1
  OR10G8 WILD-TYPE  9 12
  OR10G8 MUTATED OR10G8 WILD-TYPE 
               1               21 
  OR10G8 MUTATED OR10G8 WILD-TYPE 
               1               12 
$`OR10G8 MUTATED`
TCGA-DA-A3F3 
           7 

$`OR10G8 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        2.43         8.09        25.28        23.90         9.67         3.52 
TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       42.84        16.21        15.39 

  OR10G8 MUTATED OR10G8 WILD-TYPE 
            7.00             1.08 
  OR10G8 MUTATED OR10G8 WILD-TYPE 
            7.00            48.79 
  OR10G8 MUTATED OR10G8 WILD-TYPE 
            7.00             9.99 
[1] "7.0 - 7.0 (7.0)"   "1.1 - 48.8 (10.0)"
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE"   "OR10G8 MUTATED" "OR10G8 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE"   "OR10G8 MUTATED" "OR10G8 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE"   "OR10G8 MUTATED" "OR10G8 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
[1] "Remove cluster labels:" "OR10G8 MUTATED"        
clus
  OR10G8 MUTATED OR10G8 WILD-TYPE 
               1               21 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-EE-A17X       TCGA-EE-A185 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R       TCGA-EE-A29S 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1       TCGA-EE-A2A2 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N       TCGA-GN-A267 
"OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" "OR10G8 WILD-TYPE" 
      TCGA-GN-A268 
"OR10G8 WILD-TYPE" 
D30V2, continuous
                  vv
clus               DISTANT METASTASIS
  OR10G8 MUTATED                    1
  OR10G8 WILD-TYPE                  7
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  OR10G8 MUTATED                                                                                          1
  OR10G8 WILD-TYPE                                                                                        8
                  vv
clus               REGIONAL LYMPH NODE
  OR10G8 MUTATED                     2
  OR10G8 WILD-TYPE                  26
D30V3, multiclass
                                                                                          clus
vv                                                                                         OR10G8 MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   2
                                                                                          clus
vv                                                                                         OR10G8 WILD-TYPE
  DISTANT METASTASIS                                                                                      7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    26
D30V4, binary
                  cls
clus                0  1
  OR10G8 MUTATED    3  1
  OR10G8 WILD-TYPE 13 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10G8 MUTATED      3    1
  OR10G8 WILD-TYPE   13   28
        clus
vv       OR10G8 MUTATED OR10G8 WILD-TYPE
  FEMALE              3               13
  MALE                1               28
                  vv
clus               N0 N1A N1B N2A N2B N3
  OR10G8 MUTATED    2   0   0   0   1  0
  OR10G8 WILD-TYPE 25   3   4   1   1  5
D30V5, multiclass
D30V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  OR10G8 MUTATED             0       1        0        0        0         0
  OR10G8 WILD-TYPE           1       2        4        6        4         3
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  OR10G8 MUTATED           0         1         0          0          1
  OR10G8 WILD-TYPE         4         1         1          1          5
                  vv
clus               STAGE IIIC STAGE IV
  OR10G8 MUTATED            0        0
  OR10G8 WILD-TYPE          6        1
D30V7, multiclass

Clustering(31) Variable = UGT2B4 MUTATION ANALYSIS
D31V1, survival
                  sevent
clus2               0  1
  UGT2B4 MUTATED    1  2
  UGT2B4 WILD-TYPE  8 11
  UGT2B4 MUTATED UGT2B4 WILD-TYPE 
               3               19 
  UGT2B4 MUTATED UGT2B4 WILD-TYPE 
               2               11 
$`UGT2B4 MUTATED`
TCGA-DA-A1HV TCGA-EE-A17X TCGA-GN-A267 
       48.79        11.57        16.21 

$`UGT2B4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        4.27         1.08         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A268 
       15.39 

  UGT2B4 MUTATED UGT2B4 WILD-TYPE 
           11.57             1.08 
  UGT2B4 MUTATED UGT2B4 WILD-TYPE 
           48.79            42.84 
  UGT2B4 MUTATED UGT2B4 WILD-TYPE 
           16.21             8.84 
[1] "11.6 - 48.8 (16.2)" "1.1 - 42.8 (8.8)"  
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "UGT2B4 MUTATED" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE"   "UGT2B4 MUTATED" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
  "UGT2B4 MUTATED" "UGT2B4 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "UGT2B4 MUTATED" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE"   "UGT2B4 MUTATED" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
  "UGT2B4 MUTATED" "UGT2B4 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "UGT2B4 MUTATED" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE"   "UGT2B4 MUTATED" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" "UGT2B4 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
  "UGT2B4 MUTATED" "UGT2B4 WILD-TYPE" 
[1] "hr=" "1.4"
D31V2, continuous
                  vv
clus               DISTANT METASTASIS
  UGT2B4 MUTATED                    1
  UGT2B4 WILD-TYPE                  7
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  UGT2B4 MUTATED                                                                                          1
  UGT2B4 WILD-TYPE                                                                                        8
                  vv
clus               REGIONAL LYMPH NODE
  UGT2B4 MUTATED                     6
  UGT2B4 WILD-TYPE                  22
D31V3, multiclass
                                                                                          clus
vv                                                                                         UGT2B4 MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   6
                                                                                          clus
vv                                                                                         UGT2B4 WILD-TYPE
  DISTANT METASTASIS                                                                                      7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    22
D31V4, binary
                  cls
clus                0  1
  UGT2B4 MUTATED    4  4
  UGT2B4 WILD-TYPE 12 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2B4 MUTATED      4    4
  UGT2B4 WILD-TYPE   12   25
        clus
vv       UGT2B4 MUTATED UGT2B4 WILD-TYPE
  FEMALE              4               12
  MALE                4               25
                  vv
clus               N0 N1A N1B N2A N2B N3
  UGT2B4 MUTATED    5   1   0   0   1  0
  UGT2B4 WILD-TYPE 22   2   4   1   1  5
D31V5, multiclass
D31V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  UGT2B4 MUTATED             0       0        3        0        1         0
  UGT2B4 WILD-TYPE           1       3        1        6        3         3
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  UGT2B4 MUTATED           1         0         0          1          1
  UGT2B4 WILD-TYPE         3         2         1          0          5
                  vv
clus               STAGE IIIC STAGE IV
  UGT2B4 MUTATED            0        0
  UGT2B4 WILD-TYPE          6        1
D31V7, multiclass

Clustering(32) Variable = ZBBX MUTATION ANALYSIS
D32V1, survival
                sevent
clus2             0  1
  ZBBX MUTATED    3  1
  ZBBX WILD-TYPE  6 12
  ZBBX MUTATED ZBBX WILD-TYPE 
             4             18 
  ZBBX MUTATED ZBBX WILD-TYPE 
             1             12 
$`ZBBX MUTATED`
TCGA-DA-A1I1 TCGA-EE-A29L TCGA-EE-A2A2 TCGA-ER-A19N 
       39.19         1.08        23.90        42.84 

$`ZBBX WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        48.79         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       11.57         4.27         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A267 TCGA-GN-A268 
        8.09        25.28         9.67         3.52        16.21        15.39 

  ZBBX MUTATED ZBBX WILD-TYPE 
          1.08           2.43 
  ZBBX MUTATED ZBBX WILD-TYPE 
         42.84          48.79 
  ZBBX MUTATED ZBBX WILD-TYPE 
        31.545          9.255 
[1] "1.1 - 42.8 (31.5)" "2.4 - 48.8 (9.3)" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"ZBBX WILD-TYPE" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"ZBBX WILD-TYPE"   "ZBBX MUTATED" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"ZBBX WILD-TYPE"   "ZBBX MUTATED" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"ZBBX WILD-TYPE" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
  "ZBBX MUTATED" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE"   "ZBBX MUTATED" 
    TCGA-GN-A267     TCGA-GN-A268 
"ZBBX WILD-TYPE" "ZBBX WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"ZBBX WILD-TYPE" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"ZBBX WILD-TYPE"   "ZBBX MUTATED" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"ZBBX WILD-TYPE"   "ZBBX MUTATED" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"ZBBX WILD-TYPE" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
  "ZBBX MUTATED" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE"   "ZBBX MUTATED" 
    TCGA-GN-A267     TCGA-GN-A268 
"ZBBX WILD-TYPE" "ZBBX WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"ZBBX WILD-TYPE" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"ZBBX WILD-TYPE"   "ZBBX MUTATED" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"ZBBX WILD-TYPE"   "ZBBX MUTATED" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"ZBBX WILD-TYPE" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
  "ZBBX MUTATED" "ZBBX WILD-TYPE" "ZBBX WILD-TYPE"   "ZBBX MUTATED" 
    TCGA-GN-A267     TCGA-GN-A268 
"ZBBX WILD-TYPE" "ZBBX WILD-TYPE" 
[1] "hr=" "4.6"
D32V2, continuous
                vv
clus             DISTANT METASTASIS
  ZBBX MUTATED                    1
  ZBBX WILD-TYPE                  7
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ZBBX MUTATED                                                                                          1
  ZBBX WILD-TYPE                                                                                        8
                vv
clus             REGIONAL LYMPH NODE
  ZBBX MUTATED                     7
  ZBBX WILD-TYPE                  21
D32V3, multiclass
                                                                                          clus
vv                                                                                         ZBBX MUTATED
  DISTANT METASTASIS                                                                                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            1
  REGIONAL LYMPH NODE                                                                                 7
                                                                                          clus
vv                                                                                         ZBBX WILD-TYPE
  DISTANT METASTASIS                                                                                    7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              8
  REGIONAL LYMPH NODE                                                                                  21
D32V4, binary
                cls
clus              0  1
  ZBBX MUTATED    1  8
  ZBBX WILD-TYPE 15 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZBBX MUTATED      1    8
  ZBBX WILD-TYPE   15   21
        clus
vv       ZBBX MUTATED ZBBX WILD-TYPE
  FEMALE            1             15
  MALE              8             21
                vv
clus             N0 N1A N1B N2A N2B N3
  ZBBX MUTATED    2   1   1   0   0  2
  ZBBX WILD-TYPE 25   2   3   1   2  3
D32V5, multiclass
D32V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ZBBX MUTATED             0       0        0        0        2         0
  ZBBX WILD-TYPE           1       3        4        6        2         3
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ZBBX MUTATED           0         0         0          0          2          2
  ZBBX WILD-TYPE         4         2         1          1          4          4
                vv
clus             STAGE IV
  ZBBX MUTATED          0
  ZBBX WILD-TYPE        1
D32V7, multiclass

Clustering(33) Variable = C1QTNF9 MUTATION ANALYSIS
D33V1, survival
                   sevent
clus2                0  1
  C1QTNF9 MUTATED    1  0
  C1QTNF9 WILD-TYPE  8 13
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
                1                21 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
                0                13 
$`C1QTNF9 MUTATED`
TCGA-EE-A2A1 
       25.28 

$`C1QTNF9 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
        7.00        11.57         4.27         1.08         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        9.99         2.43         8.09        23.90         9.67         3.52 
TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       42.84        16.21        15.39 

  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
            25.28              1.08 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
            25.28             48.79 
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
            25.28              9.67 
[1] "25.3 - 25.3 (25.3)" "1.1 - 48.8 (9.7)"  
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE"   "C1QTNF9 MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE"   "C1QTNF9 MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE"   "C1QTNF9 MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
[1] "Remove cluster labels:" "C1QTNF9 MUTATED"       
clus
  C1QTNF9 MUTATED C1QTNF9 WILD-TYPE 
                1                21 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A2 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N        TCGA-GN-A267 
"C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" "C1QTNF9 WILD-TYPE" 
       TCGA-GN-A268 
"C1QTNF9 WILD-TYPE" 
D33V2, continuous
                   vv
clus                DISTANT METASTASIS
  C1QTNF9 MUTATED                    0
  C1QTNF9 WILD-TYPE                  8
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  C1QTNF9 MUTATED                                                                                          1
  C1QTNF9 WILD-TYPE                                                                                        8
                   vv
clus                REGIONAL LYMPH NODE
  C1QTNF9 MUTATED                     2
  C1QTNF9 WILD-TYPE                  26
D33V3, multiclass
                                                                                          clus
vv                                                                                         C1QTNF9 MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         C1QTNF9 WILD-TYPE
  DISTANT METASTASIS                                                                                       8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 8
  REGIONAL LYMPH NODE                                                                                     26
D33V4, binary
                   cls
clus                 0  1
  C1QTNF9 MUTATED    1  2
  C1QTNF9 WILD-TYPE 15 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1QTNF9 MUTATED      1    2
  C1QTNF9 WILD-TYPE   15   27
        clus
vv       C1QTNF9 MUTATED C1QTNF9 WILD-TYPE
  FEMALE               1                15
  MALE                 2                27
                   vv
clus                N0 N1A N1B N2A N2B N3
  C1QTNF9 MUTATED    3   0   0   0   0  0
  C1QTNF9 WILD-TYPE 24   3   4   1   2  5
D33V5, multiclass
D33V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  C1QTNF9 MUTATED             0       0        0        1        1         0
  C1QTNF9 WILD-TYPE           1       3        4        5        3         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  C1QTNF9 MUTATED           0         1         0          0          0
  C1QTNF9 WILD-TYPE         4         1         1          1          6
                   vv
clus                STAGE IIIC STAGE IV
  C1QTNF9 MUTATED            0        0
  C1QTNF9 WILD-TYPE          6        1
D33V7, multiclass

Clustering(34) Variable = HCRTR2 MUTATION ANALYSIS
D34V1, survival
                  sevent
clus2               0  1
  HCRTR2 MUTATED    2  1
  HCRTR2 WILD-TYPE  7 12
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               3               19 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               1               12 
$`HCRTR2 MUTATED`
TCGA-DA-A1HV TCGA-EE-A2A2 TCGA-GN-A268 
       48.79        23.90        15.39 

$`HCRTR2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        2.43         8.09        25.28         9.67         3.52        42.84 
TCGA-GN-A267 
       16.21 

  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
           15.39             1.08 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
           48.79            42.84 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
           23.90             8.84 
[1] "15.4 - 48.8 (23.9)" "1.1 - 42.8 (8.8)"  
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "HCRTR2 MUTATED" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "HCRTR2 MUTATED" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"HCRTR2 WILD-TYPE"   "HCRTR2 MUTATED" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "HCRTR2 MUTATED" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "HCRTR2 MUTATED" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"HCRTR2 WILD-TYPE"   "HCRTR2 MUTATED" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "HCRTR2 MUTATED" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "HCRTR2 MUTATED" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" "HCRTR2 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"HCRTR2 WILD-TYPE"   "HCRTR2 MUTATED" 
[1] "hr=" "3.4"
D34V2, continuous
                  vv
clus               DISTANT METASTASIS
  HCRTR2 MUTATED                    0
  HCRTR2 WILD-TYPE                  8
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  HCRTR2 MUTATED                                                                                          1
  HCRTR2 WILD-TYPE                                                                                        8
                  vv
clus               REGIONAL LYMPH NODE
  HCRTR2 MUTATED                     6
  HCRTR2 WILD-TYPE                  22
D34V3, multiclass
                                                                                          clus
vv                                                                                         HCRTR2 MUTATED
  DISTANT METASTASIS                                                                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   6
                                                                                          clus
vv                                                                                         HCRTR2 WILD-TYPE
  DISTANT METASTASIS                                                                                      8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    22
D34V4, binary
                  cls
clus                0  1
  HCRTR2 MUTATED    2  5
  HCRTR2 WILD-TYPE 14 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED      2    5
  HCRTR2 WILD-TYPE   14   24
        clus
vv       HCRTR2 MUTATED HCRTR2 WILD-TYPE
  FEMALE              2               14
  MALE                5               24
                  vv
clus               N0 N1A N1B N2A N2B N3
  HCRTR2 MUTATED    4   1   1   0   1  0
  HCRTR2 WILD-TYPE 23   2   3   1   1  5
D34V5, multiclass
D34V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  HCRTR2 MUTATED             0       0        1        0        2         0
  HCRTR2 WILD-TYPE           1       3        3        6        2         3
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  HCRTR2 MUTATED           1         0         0          0          3
  HCRTR2 WILD-TYPE         3         2         1          1          3
                  vv
clus               STAGE IIIC STAGE IV
  HCRTR2 MUTATED            0        0
  HCRTR2 WILD-TYPE          6        1
D34V7, multiclass

Clustering(35) Variable = KRT78 MUTATION ANALYSIS
D35V1, survival
                 sevent
clus2              0  1
  KRT78 MUTATED    2  1
  KRT78 WILD-TYPE  7 12
  KRT78 MUTATED KRT78 WILD-TYPE 
              3              19 
  KRT78 MUTATED KRT78 WILD-TYPE 
              1              12 
$`KRT78 MUTATED`
TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A2A1 
       48.79        11.57        25.28 

$`KRT78 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        4.27         1.08         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
        8.09        23.90         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  KRT78 MUTATED KRT78 WILD-TYPE 
          11.57            1.08 
  KRT78 MUTATED KRT78 WILD-TYPE 
          48.79           42.84 
  KRT78 MUTATED KRT78 WILD-TYPE 
          25.28            8.84 
[1] "11.6 - 48.8 (25.3)" "1.1 - 42.8 (8.8)"  
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "KRT78 MUTATED" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE"   "KRT78 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE"   "KRT78 MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"KRT78 WILD-TYPE" "KRT78 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "KRT78 MUTATED" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE"   "KRT78 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE"   "KRT78 MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"KRT78 WILD-TYPE" "KRT78 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "KRT78 MUTATED" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE"   "KRT78 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE"   "KRT78 MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" "KRT78 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"KRT78 WILD-TYPE" "KRT78 WILD-TYPE" 
[1] "hr=" "3.2"
D35V2, continuous
                 vv
clus              DISTANT METASTASIS
  KRT78 MUTATED                    0
  KRT78 WILD-TYPE                  8
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  KRT78 MUTATED                                                                                          1
  KRT78 WILD-TYPE                                                                                        8
                 vv
clus              REGIONAL LYMPH NODE
  KRT78 MUTATED                     4
  KRT78 WILD-TYPE                  24
D35V3, multiclass
                                                                                          clus
vv                                                                                         KRT78 MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  4
                                                                                          clus
vv                                                                                         KRT78 WILD-TYPE
  DISTANT METASTASIS                                                                                     8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               8
  REGIONAL LYMPH NODE                                                                                   24
D35V4, binary
                 cls
clus               0  1
  KRT78 MUTATED    2  3
  KRT78 WILD-TYPE 14 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT78 MUTATED      2    3
  KRT78 WILD-TYPE   14   26
        clus
vv       KRT78 MUTATED KRT78 WILD-TYPE
  FEMALE             2              14
  MALE               3              26
                 vv
clus              N0 N1A N1B N2A N2B N3
  KRT78 MUTATED    4   0   0   0   1  0
  KRT78 WILD-TYPE 23   3   4   1   1  5
D35V5, multiclass
D35V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  KRT78 MUTATED             0       0        2        1        0         0
  KRT78 WILD-TYPE           1       3        2        5        4         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  KRT78 MUTATED           0         1         0          0          1
  KRT78 WILD-TYPE         4         1         1          1          5
                 vv
clus              STAGE IIIC STAGE IV
  KRT78 MUTATED            0        0
  KRT78 WILD-TYPE          6        1
D35V7, multiclass

Clustering(36) Variable = BCLAF1 MUTATION ANALYSIS
D36V1, survival
                  sevent
clus2               0  1
  BCLAF1 MUTATED    3  1
  BCLAF1 WILD-TYPE  6 12
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               4               18 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               1               12 
$`BCLAF1 MUTATED`
TCGA-DA-A1HV TCGA-EE-A29L TCGA-EE-A2A2 TCGA-ER-A19N 
       48.79         1.08        23.90        42.84 

$`BCLAF1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       11.57         4.27         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A267 TCGA-GN-A268 
        8.09        25.28         9.67         3.52        16.21        15.39 

  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
            1.08             2.43 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
           48.79            39.19 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
          33.370            9.255 
[1] "1.1 - 48.8 (33.4)" "2.4 - 39.2 (9.3)" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "BCLAF1 MUTATED" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"BCLAF1 WILD-TYPE"   "BCLAF1 MUTATED" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "BCLAF1 MUTATED" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE"   "BCLAF1 MUTATED" 
      TCGA-GN-A267       TCGA-GN-A268 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "BCLAF1 MUTATED" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"BCLAF1 WILD-TYPE"   "BCLAF1 MUTATED" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "BCLAF1 MUTATED" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE"   "BCLAF1 MUTATED" 
      TCGA-GN-A267       TCGA-GN-A268 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "BCLAF1 MUTATED" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"BCLAF1 WILD-TYPE"   "BCLAF1 MUTATED" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "BCLAF1 MUTATED" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE"   "BCLAF1 MUTATED" 
      TCGA-GN-A267       TCGA-GN-A268 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
[1] "hr=" "4.6"
D36V2, continuous
                  vv
clus               DISTANT METASTASIS
  BCLAF1 MUTATED                    0
  BCLAF1 WILD-TYPE                  8
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  BCLAF1 MUTATED                                                                                          2
  BCLAF1 WILD-TYPE                                                                                        7
                  vv
clus               REGIONAL LYMPH NODE
  BCLAF1 MUTATED                     7
  BCLAF1 WILD-TYPE                  21
D36V3, multiclass
                                                                                          clus
vv                                                                                         BCLAF1 MUTATED
  DISTANT METASTASIS                                                                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              2
  REGIONAL LYMPH NODE                                                                                   7
                                                                                          clus
vv                                                                                         BCLAF1 WILD-TYPE
  DISTANT METASTASIS                                                                                      8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                7
  REGIONAL LYMPH NODE                                                                                    21
D36V4, binary
                  cls
clus                0  1
  BCLAF1 MUTATED    2  7
  BCLAF1 WILD-TYPE 14 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      2    7
  BCLAF1 WILD-TYPE   14   22
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  FEMALE              2               14
  MALE                7               22
                  vv
clus               N0 N1A N1B N2A N2B N3
  BCLAF1 MUTATED    4   1   1   0   1  1
  BCLAF1 WILD-TYPE 23   2   3   1   1  4
D36V5, multiclass
D36V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  BCLAF1 MUTATED             0       1        1        0        1         0
  BCLAF1 WILD-TYPE           1       2        3        6        3         3
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  BCLAF1 MUTATED           1         0         0          0          3
  BCLAF1 WILD-TYPE         3         2         1          1          3
                  vv
clus               STAGE IIIC STAGE IV
  BCLAF1 MUTATED            1        0
  BCLAF1 WILD-TYPE          5        1
D36V7, multiclass

Clustering(37) Variable = LPAR1 MUTATION ANALYSIS
D37V1, survival
                 sevent
clus2              0  1
  LPAR1 MUTATED    1  1
  LPAR1 WILD-TYPE  8 12
  LPAR1 MUTATED LPAR1 WILD-TYPE 
              2              20 
  LPAR1 MUTATED LPAR1 WILD-TYPE 
              1              12 
$`LPAR1 MUTATED`
TCGA-EE-A29S TCGA-EE-A29V 
        9.99         2.43 

$`LPAR1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
        7.00        11.57         4.27         1.08         8.12         8.84 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  LPAR1 MUTATED LPAR1 WILD-TYPE 
           2.43            1.08 
  LPAR1 MUTATED LPAR1 WILD-TYPE 
           9.99           48.79 
  LPAR1 MUTATED LPAR1 WILD-TYPE 
           6.21           10.62 
[1] "2.4 - 10.0 (6.2)"  "1.1 - 48.8 (10.6)"
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "LPAR1 MUTATED"   "LPAR1 MUTATED" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "LPAR1 MUTATED"   "LPAR1 MUTATED" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "LPAR1 MUTATED"   "LPAR1 MUTATED" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
[1] "Remove cluster labels:" "LPAR1 MUTATED"         
clus
  LPAR1 MUTATED LPAR1 WILD-TYPE 
              2              20 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-EE-A29X      TCGA-EE-A2A1      TCGA-EE-A2A2      TCGA-EE-A2A5 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
     TCGA-ER-A19D      TCGA-ER-A19N      TCGA-GN-A267      TCGA-GN-A268 
"LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" "LPAR1 WILD-TYPE" 
D37V2, continuous
                 vv
clus              DISTANT METASTASIS
  LPAR1 MUTATED                    1
  LPAR1 WILD-TYPE                  7
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  LPAR1 MUTATED                                                                                          0
  LPAR1 WILD-TYPE                                                                                        9
                 vv
clus              REGIONAL LYMPH NODE
  LPAR1 MUTATED                     2
  LPAR1 WILD-TYPE                  26
D37V3, multiclass
                                                                                          clus
vv                                                                                         LPAR1 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
  REGIONAL LYMPH NODE                                                                                  2
                                                                                          clus
vv                                                                                         LPAR1 WILD-TYPE
  DISTANT METASTASIS                                                                                     7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               9
  REGIONAL LYMPH NODE                                                                                   26
D37V4, binary
                 cls
clus               0  1
  LPAR1 MUTATED    0  3
  LPAR1 WILD-TYPE 16 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPAR1 MUTATED      0    3
  LPAR1 WILD-TYPE   16   26
        clus
vv       LPAR1 MUTATED LPAR1 WILD-TYPE
  FEMALE             0              16
  MALE               3              26
                 vv
clus              N0 N1A N1B N2A N2B N3
  LPAR1 MUTATED    2   0   1   0   0  0
  LPAR1 WILD-TYPE 25   3   3   1   2  5
D37V5, multiclass
D37V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  LPAR1 MUTATED             0       0        0        0        1         1
  LPAR1 WILD-TYPE           1       3        4        6        3         2
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  LPAR1 MUTATED           0         0         0          0          0
  LPAR1 WILD-TYPE         4         2         1          1          6
                 vv
clus              STAGE IIIC STAGE IV
  LPAR1 MUTATED            1        0
  LPAR1 WILD-TYPE          5        1
D37V7, multiclass

Clustering(38) Variable = STK31 MUTATION ANALYSIS
D38V1, survival
                 sevent
clus2              0  1
  STK31 MUTATED    4  1
  STK31 WILD-TYPE  5 12
  STK31 MUTATED STK31 WILD-TYPE 
              5              17 
  STK31 MUTATED STK31 WILD-TYPE 
              1              12 
$`STK31 MUTATED`
TCGA-DA-A1HV TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19N 
       48.79         8.09        25.28        23.90        42.84 

$`STK31 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A267 TCGA-GN-A268 
        2.43         9.67         3.52        16.21        15.39 

  STK31 MUTATED STK31 WILD-TYPE 
           8.09            1.08 
  STK31 MUTATED STK31 WILD-TYPE 
          48.79           39.19 
  STK31 MUTATED STK31 WILD-TYPE 
          25.28            8.84 
[1] "8.1 - 48.8 (25.3)" "1.1 - 39.2 (8.8)" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"STK31 WILD-TYPE" "STK31 WILD-TYPE" "STK31 WILD-TYPE" "STK31 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "STK31 MUTATED" "STK31 WILD-TYPE" "STK31 WILD-TYPE" "STK31 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"STK31 WILD-TYPE" "STK31 WILD-TYPE" "STK31 WILD-TYPE" "STK31 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"STK31 WILD-TYPE" "STK31 WILD-TYPE"   "STK31 MUTATED"   "STK31 MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "STK31 MUTATED" "STK31 WILD-TYPE" "STK31 WILD-TYPE"   "STK31 MUTATED" 
     TCGA-GN-A267      TCGA-GN-A268 
"STK31 WILD-TYPE" "STK31 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"STK31 WILD-TYPE" "STK31 WILD-TYPE" "STK31 WILD-TYPE" "STK31 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "STK31 MUTATED" "STK31 WILD-TYPE" "STK31 WILD-TYPE" "STK31 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"STK31 WILD-TYPE" "STK31 WILD-TYPE" "STK31 WILD-TYPE" "STK31 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"STK31 WILD-TYPE" "STK31 WILD-TYPE"   "STK31 MUTATED"   "STK31 MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "STK31 MUTATED" "STK31 WILD-TYPE" "STK31 WILD-TYPE"   "STK31 MUTATED" 
     TCGA-GN-A267      TCGA-GN-A268 
"STK31 WILD-TYPE" "STK31 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"STK31 WILD-TYPE" "STK31 WILD-TYPE" "STK31 WILD-TYPE" "STK31 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "STK31 MUTATED" "STK31 WILD-TYPE" "STK31 WILD-TYPE" "STK31 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"STK31 WILD-TYPE" "STK31 WILD-TYPE" "STK31 WILD-TYPE" "STK31 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"STK31 WILD-TYPE" "STK31 WILD-TYPE"   "STK31 MUTATED"   "STK31 MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "STK31 MUTATED" "STK31 WILD-TYPE" "STK31 WILD-TYPE"   "STK31 MUTATED" 
     TCGA-GN-A267      TCGA-GN-A268 
"STK31 WILD-TYPE" "STK31 WILD-TYPE" 
[1] "hr=" "7.1"
D38V2, continuous
                 vv
clus              DISTANT METASTASIS
  STK31 MUTATED                    0
  STK31 WILD-TYPE                  8
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  STK31 MUTATED                                                                                          0
  STK31 WILD-TYPE                                                                                        9
                 vv
clus              REGIONAL LYMPH NODE
  STK31 MUTATED                     6
  STK31 WILD-TYPE                  22
D38V3, multiclass
                                                                                          clus
vv                                                                                         STK31 MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
  REGIONAL LYMPH NODE                                                                                  6
                                                                                          clus
vv                                                                                         STK31 WILD-TYPE
  DISTANT METASTASIS                                                                                     8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               9
  REGIONAL LYMPH NODE                                                                                   22
D38V4, binary
                 cls
clus               0  1
  STK31 MUTATED    2  4
  STK31 WILD-TYPE 14 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK31 MUTATED      2    4
  STK31 WILD-TYPE   14   25
        clus
vv       STK31 MUTATED STK31 WILD-TYPE
  FEMALE             2              14
  MALE               4              25
                 vv
clus              N0 N1A N1B N2A N2B N3
  STK31 MUTATED    3   0   1   0   1  0
  STK31 WILD-TYPE 24   3   3   1   1  5
D38V5, multiclass
D38V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  STK31 MUTATED             0       0        0        2        1         0
  STK31 WILD-TYPE           1       3        4        4        3         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  STK31 MUTATED           0         0         0          0          2
  STK31 WILD-TYPE         4         2         1          1          4
                 vv
clus              STAGE IIIC STAGE IV
  STK31 MUTATED            0        0
  STK31 WILD-TYPE          6        1
D38V7, multiclass

Clustering(39) Variable = HBG2 MUTATION ANALYSIS
D39V1, survival
                sevent
clus2             0  1
  HBG2 MUTATED    1  1
  HBG2 WILD-TYPE  8 12
  HBG2 MUTATED HBG2 WILD-TYPE 
             2             20 
  HBG2 MUTATED HBG2 WILD-TYPE 
             1             12 
$`HBG2 MUTATED`
TCGA-EE-A29S TCGA-EE-A29V 
        9.99         2.43 

$`HBG2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
        7.00        11.57         4.27         1.08         8.12         8.84 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  HBG2 MUTATED HBG2 WILD-TYPE 
          2.43           1.08 
  HBG2 MUTATED HBG2 WILD-TYPE 
          9.99          48.79 
  HBG2 MUTATED HBG2 WILD-TYPE 
          6.21          10.62 
[1] "2.4 - 10.0 (6.2)"  "1.1 - 48.8 (10.6)"
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
  "HBG2 MUTATED"   "HBG2 MUTATED" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
  "HBG2 MUTATED"   "HBG2 MUTATED" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
  "HBG2 MUTATED"   "HBG2 MUTATED" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
[1] "Remove cluster labels:" "HBG2 MUTATED"          
clus
  HBG2 MUTATED HBG2 WILD-TYPE 
             2             20 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-EE-A29X     TCGA-EE-A2A1     TCGA-EE-A2A2     TCGA-EE-A2A5 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
    TCGA-ER-A19D     TCGA-ER-A19N     TCGA-GN-A267     TCGA-GN-A268 
"HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" "HBG2 WILD-TYPE" 
D39V2, continuous
                vv
clus             DISTANT METASTASIS
  HBG2 MUTATED                    1
  HBG2 WILD-TYPE                  7
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  HBG2 MUTATED                                                                                          1
  HBG2 WILD-TYPE                                                                                        8
                vv
clus             REGIONAL LYMPH NODE
  HBG2 MUTATED                     2
  HBG2 WILD-TYPE                  26
D39V3, multiclass
                                                                                          clus
vv                                                                                         HBG2 MUTATED
  DISTANT METASTASIS                                                                                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            1
  REGIONAL LYMPH NODE                                                                                 2
                                                                                          clus
vv                                                                                         HBG2 WILD-TYPE
  DISTANT METASTASIS                                                                                    7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              8
  REGIONAL LYMPH NODE                                                                                  26
D39V4, binary
                cls
clus              0  1
  HBG2 MUTATED    1  3
  HBG2 WILD-TYPE 15 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  HBG2 MUTATED      1    3
  HBG2 WILD-TYPE   15   26
        clus
vv       HBG2 MUTATED HBG2 WILD-TYPE
  FEMALE            1             15
  MALE              3             26
                vv
clus             N0 N1A N1B N2A N2B N3
  HBG2 MUTATED    3   0   1   0   0  0
  HBG2 WILD-TYPE 24   3   3   1   2  5
D39V5, multiclass
D39V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  HBG2 MUTATED             0       0        0        0        1         1
  HBG2 WILD-TYPE           1       3        4        6        3         2
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  HBG2 MUTATED           0         1         0          0          0          1
  HBG2 WILD-TYPE         4         1         1          1          6          5
                vv
clus             STAGE IV
  HBG2 MUTATED          0
  HBG2 WILD-TYPE        1
D39V7, multiclass

Clustering(40) Variable = BAGE2 MUTATION ANALYSIS
D40V1, survival
                 sevent
clus2              0  1
  BAGE2 MUTATED    0  1
  BAGE2 WILD-TYPE  9 12
  BAGE2 MUTATED BAGE2 WILD-TYPE 
              1              21 
  BAGE2 MUTATED BAGE2 WILD-TYPE 
              1              12 
$`BAGE2 MUTATED`
TCGA-EE-A185 
        4.27 

$`BAGE2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        7.00        11.57         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        2.43         8.09        25.28        23.90         9.67         3.52 
TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       42.84        16.21        15.39 

  BAGE2 MUTATED BAGE2 WILD-TYPE 
           4.27            1.08 
  BAGE2 MUTATED BAGE2 WILD-TYPE 
           4.27           48.79 
  BAGE2 MUTATED BAGE2 WILD-TYPE 
           4.27            9.99 
[1] "4.3 - 4.3 (4.3)"   "1.1 - 48.8 (10.0)"
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
  "BAGE2 MUTATED" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
  "BAGE2 MUTATED" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
  "BAGE2 MUTATED" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
[1] "Remove cluster labels:" "BAGE2 MUTATED"         
clus
  BAGE2 MUTATED BAGE2 WILD-TYPE 
              1              21 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R      TCGA-EE-A29S 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1      TCGA-EE-A2A2 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N      TCGA-GN-A267 
"BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" "BAGE2 WILD-TYPE" 
     TCGA-GN-A268 
"BAGE2 WILD-TYPE" 
D40V2, continuous
                 vv
clus              DISTANT METASTASIS
  BAGE2 MUTATED                    2
  BAGE2 WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  BAGE2 MUTATED                                                                                          0
  BAGE2 WILD-TYPE                                                                                        9
                 vv
clus              REGIONAL LYMPH NODE
  BAGE2 MUTATED                     1
  BAGE2 WILD-TYPE                  27
D40V3, multiclass
                                                                                          clus
vv                                                                                         BAGE2 MUTATED
  DISTANT METASTASIS                                                                                   2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
  REGIONAL LYMPH NODE                                                                                  1
                                                                                          clus
vv                                                                                         BAGE2 WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               9
  REGIONAL LYMPH NODE                                                                                   27
D40V4, binary
                 cls
clus               0  1
  BAGE2 MUTATED    1  2
  BAGE2 WILD-TYPE 15 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAGE2 MUTATED      1    2
  BAGE2 WILD-TYPE   15   27
        clus
vv       BAGE2 MUTATED BAGE2 WILD-TYPE
  FEMALE             1              15
  MALE               2              27
                 vv
clus              N0 N1A N1B N2A N2B N3
  BAGE2 MUTATED    2   0   0   0   0  1
  BAGE2 WILD-TYPE 25   3   4   1   2  4
D40V5, multiclass
D40V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  BAGE2 MUTATED             0       0        0        0        1         0
  BAGE2 WILD-TYPE           1       3        4        6        3         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  BAGE2 MUTATED           0         1         0          0          0
  BAGE2 WILD-TYPE         4         1         1          1          6
                 vv
clus              STAGE IIIC STAGE IV
  BAGE2 MUTATED            1        0
  BAGE2 WILD-TYPE          5        1
D40V7, multiclass

Clustering(41) Variable = ADH1B MUTATION ANALYSIS
D41V1, survival
                 sevent
clus2              0  1
  ADH1B MUTATED    2  0
  ADH1B WILD-TYPE  7 13
  ADH1B MUTATED ADH1B WILD-TYPE 
              2              20 
  ADH1B MUTATED ADH1B WILD-TYPE 
              0              13 
$`ADH1B MUTATED`
TCGA-DA-A1I1 TCGA-EE-A29R 
       39.19         8.84 

$`ADH1B WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        48.79         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       11.57         4.27         1.08         8.12         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  ADH1B MUTATED ADH1B WILD-TYPE 
           8.84            1.08 
  ADH1B MUTATED ADH1B WILD-TYPE 
          39.19           48.79 
  ADH1B MUTATED ADH1B WILD-TYPE 
         24.015           9.830 
[1] "8.8 - 39.2 (24.0)" "1.1 - 48.8 (9.8)" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"ADH1B WILD-TYPE"   "ADH1B MUTATED" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE"   "ADH1B MUTATED" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"ADH1B WILD-TYPE"   "ADH1B MUTATED" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE"   "ADH1B MUTATED" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"ADH1B WILD-TYPE"   "ADH1B MUTATED" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE"   "ADH1B MUTATED" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
[1] "Remove cluster labels:" "ADH1B MUTATED"         
clus
  ADH1B MUTATED ADH1B WILD-TYPE 
              2              20 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A3F3      TCGA-EE-A17X      TCGA-EE-A185 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29S      TCGA-EE-A29V 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-EE-A29X      TCGA-EE-A2A1      TCGA-EE-A2A2      TCGA-EE-A2A5 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
     TCGA-ER-A19D      TCGA-ER-A19N      TCGA-GN-A267      TCGA-GN-A268 
"ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" "ADH1B WILD-TYPE" 
D41V2, continuous
                 vv
clus              DISTANT METASTASIS
  ADH1B MUTATED                    2
  ADH1B WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ADH1B MUTATED                                                                                          1
  ADH1B WILD-TYPE                                                                                        8
                 vv
clus              REGIONAL LYMPH NODE
  ADH1B MUTATED                     3
  ADH1B WILD-TYPE                  25
D41V3, multiclass
                                                                                          clus
vv                                                                                         ADH1B MUTATED
  DISTANT METASTASIS                                                                                   2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         ADH1B WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               8
  REGIONAL LYMPH NODE                                                                                   25
D41V4, binary
                 cls
clus               0  1
  ADH1B MUTATED    3  3
  ADH1B WILD-TYPE 13 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADH1B MUTATED      3    3
  ADH1B WILD-TYPE   13   26
        clus
vv       ADH1B MUTATED ADH1B WILD-TYPE
  FEMALE             3              13
  MALE               3              26
                 vv
clus              N0 N1A N1B N2A N2B N3
  ADH1B MUTATED    3   0   1   0   0  1
  ADH1B WILD-TYPE 24   3   3   1   2  4
D41V5, multiclass
D41V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ADH1B MUTATED             0       1        0        0        0         1
  ADH1B WILD-TYPE           1       2        4        6        4         2
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ADH1B MUTATED           0         1         0          0          0
  ADH1B WILD-TYPE         4         1         1          1          6
                 vv
clus              STAGE IIIC STAGE IV
  ADH1B MUTATED            2        0
  ADH1B WILD-TYPE          4        1
D41V7, multiclass

Clustering(42) Variable = CNTN4 MUTATION ANALYSIS
D42V1, survival
                 sevent
clus2              0  1
  CNTN4 MUTATED    3  3
  CNTN4 WILD-TYPE  6 10
  CNTN4 MUTATED CNTN4 WILD-TYPE 
              6              16 
  CNTN4 MUTATED CNTN4 WILD-TYPE 
              3              10 
$`CNTN4 MUTATED`
TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-ER-A19N TCGA-GN-A267 
       11.57         1.08         8.12         8.84        42.84        16.21 

$`CNTN4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A185 TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
        7.00         4.27         9.99         2.43         8.09        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A268 
       23.90         9.67         3.52        15.39 

  CNTN4 MUTATED CNTN4 WILD-TYPE 
           1.08            2.43 
  CNTN4 MUTATED CNTN4 WILD-TYPE 
          42.84           48.79 
  CNTN4 MUTATED CNTN4 WILD-TYPE 
         10.205           9.830 
[1] "1.1 - 42.8 (10.2)" "2.4 - 48.8 (9.8)" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE"   "CNTN4 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"CNTN4 WILD-TYPE"   "CNTN4 MUTATED"   "CNTN4 MUTATED"   "CNTN4 MUTATED" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE"   "CNTN4 MUTATED" 
     TCGA-GN-A267      TCGA-GN-A268 
  "CNTN4 MUTATED" "CNTN4 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE"   "CNTN4 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"CNTN4 WILD-TYPE"   "CNTN4 MUTATED"   "CNTN4 MUTATED"   "CNTN4 MUTATED" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE"   "CNTN4 MUTATED" 
     TCGA-GN-A267      TCGA-GN-A268 
  "CNTN4 MUTATED" "CNTN4 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE"   "CNTN4 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"CNTN4 WILD-TYPE"   "CNTN4 MUTATED"   "CNTN4 MUTATED"   "CNTN4 MUTATED" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE" "CNTN4 WILD-TYPE"   "CNTN4 MUTATED" 
     TCGA-GN-A267      TCGA-GN-A268 
  "CNTN4 MUTATED" "CNTN4 WILD-TYPE" 
[1] "hr=" "1.1"
D42V2, continuous
                 vv
clus              DISTANT METASTASIS
  CNTN4 MUTATED                    0
  CNTN4 WILD-TYPE                  8
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CNTN4 MUTATED                                                                                          1
  CNTN4 WILD-TYPE                                                                                        8
                 vv
clus              REGIONAL LYMPH NODE
  CNTN4 MUTATED                     9
  CNTN4 WILD-TYPE                  19
D42V3, multiclass
                                                                                          clus
vv                                                                                         CNTN4 MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  9
                                                                                          clus
vv                                                                                         CNTN4 WILD-TYPE
  DISTANT METASTASIS                                                                                     8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               8
  REGIONAL LYMPH NODE                                                                                   19
D42V4, binary
                 cls
clus               0  1
  CNTN4 MUTATED    3  7
  CNTN4 WILD-TYPE 13 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTN4 MUTATED      3    7
  CNTN4 WILD-TYPE   13   22
        clus
vv       CNTN4 MUTATED CNTN4 WILD-TYPE
  FEMALE             3              13
  MALE               7              22
                 vv
clus              N0 N1A N1B N2A N2B N3
  CNTN4 MUTATED    4   2   1   0   0  1
  CNTN4 WILD-TYPE 23   1   3   1   2  4
D42V5, multiclass
D42V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CNTN4 MUTATED             0       1        1        0        1         0
  CNTN4 WILD-TYPE           1       2        3        6        3         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CNTN4 MUTATED           1         0         0          1          1
  CNTN4 WILD-TYPE         3         2         1          0          5
                 vv
clus              STAGE IIIC STAGE IV
  CNTN4 MUTATED            2        0
  CNTN4 WILD-TYPE          4        1
D42V7, multiclass

Clustering(43) Variable = DEFA4 MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2              0  1
  DEFA4 MUTATED    0  1
  DEFA4 WILD-TYPE  9 12
  DEFA4 MUTATED DEFA4 WILD-TYPE 
              1              21 
  DEFA4 MUTATED DEFA4 WILD-TYPE 
              1              12 
$`DEFA4 MUTATED`
TCGA-EE-A29L 
        1.08 

$`DEFA4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        7.00        11.57         4.27         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        2.43         8.09        25.28        23.90         9.67         3.52 
TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       42.84        16.21        15.39 

  DEFA4 MUTATED DEFA4 WILD-TYPE 
           1.08            2.43 
  DEFA4 MUTATED DEFA4 WILD-TYPE 
           1.08           48.79 
  DEFA4 MUTATED DEFA4 WILD-TYPE 
           1.08            9.99 
[1] "1.1 - 1.1 (1.1)"   "2.4 - 48.8 (10.0)"
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"DEFA4 WILD-TYPE"   "DEFA4 MUTATED" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"DEFA4 WILD-TYPE"   "DEFA4 MUTATED" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"DEFA4 WILD-TYPE"   "DEFA4 MUTATED" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
[1] "Remove cluster labels:" "DEFA4 MUTATED"         
clus
  DEFA4 MUTATED DEFA4 WILD-TYPE 
              1              21 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29Q      TCGA-EE-A29R      TCGA-EE-A29S 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1      TCGA-EE-A2A2 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N      TCGA-GN-A267 
"DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" "DEFA4 WILD-TYPE" 
     TCGA-GN-A268 
"DEFA4 WILD-TYPE" 
D43V2, continuous
                 vv
clus              DISTANT METASTASIS
  DEFA4 MUTATED                    1
  DEFA4 WILD-TYPE                  7
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEFA4 MUTATED                                                                                          1
  DEFA4 WILD-TYPE                                                                                        8
                 vv
clus              REGIONAL LYMPH NODE
  DEFA4 MUTATED                     2
  DEFA4 WILD-TYPE                  26
D43V3, multiclass
                                                                                          clus
vv                                                                                         DEFA4 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  2
                                                                                          clus
vv                                                                                         DEFA4 WILD-TYPE
  DISTANT METASTASIS                                                                                     7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               8
  REGIONAL LYMPH NODE                                                                                   26
D43V4, binary
                 cls
clus               0  1
  DEFA4 MUTATED    2  2
  DEFA4 WILD-TYPE 14 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DEFA4 MUTATED      2    2
  DEFA4 WILD-TYPE   14   27
        clus
vv       DEFA4 MUTATED DEFA4 WILD-TYPE
  FEMALE             2              14
  MALE               2              27
                 vv
clus              N0 N1A N1B N2A N2B N3
  DEFA4 MUTATED    3   0   0   0   0  1
  DEFA4 WILD-TYPE 24   3   4   1   2  4
D43V5, multiclass
D43V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEFA4 MUTATED             1       1        0        0        0         0
  DEFA4 WILD-TYPE           0       2        4        6        4         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEFA4 MUTATED           1         0         0          0          0
  DEFA4 WILD-TYPE         3         2         1          1          6
                 vv
clus              STAGE IIIC STAGE IV
  DEFA4 MUTATED            1        0
  DEFA4 WILD-TYPE          5        1
D43V7, multiclass

Clustering(44) Variable = GFRAL MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2              0  1
  GFRAL MUTATED    1  3
  GFRAL WILD-TYPE  8 10
  GFRAL MUTATED GFRAL WILD-TYPE 
              4              18 
  GFRAL MUTATED GFRAL WILD-TYPE 
              3              10 
$`GFRAL MUTATED`
TCGA-D3-A1Q8 TCGA-EE-A29L TCGA-EE-A29Q TCGA-GN-A268 
       28.08         1.08         8.12        15.39 

$`GFRAL WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47         8.38         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       11.57         4.27         8.84         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
       25.28        23.90         9.67         3.52        42.84        16.21 

  GFRAL MUTATED GFRAL WILD-TYPE 
           1.08            2.43 
  GFRAL MUTATED GFRAL WILD-TYPE 
          28.08           48.79 
  GFRAL MUTATED GFRAL WILD-TYPE 
         11.755           9.830 
[1] "1.1 - 28.1 (11.8)" "2.4 - 48.8 (9.8)" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"GFRAL WILD-TYPE"   "GFRAL MUTATED" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"GFRAL WILD-TYPE"   "GFRAL MUTATED"   "GFRAL MUTATED" "GFRAL WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"GFRAL WILD-TYPE"   "GFRAL MUTATED" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"GFRAL WILD-TYPE"   "GFRAL MUTATED" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"GFRAL WILD-TYPE"   "GFRAL MUTATED"   "GFRAL MUTATED" "GFRAL WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"GFRAL WILD-TYPE"   "GFRAL MUTATED" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"GFRAL WILD-TYPE"   "GFRAL MUTATED" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"GFRAL WILD-TYPE"   "GFRAL MUTATED"   "GFRAL MUTATED" "GFRAL WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" "GFRAL WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"GFRAL WILD-TYPE"   "GFRAL MUTATED" 
[1] "hr=" "1.4"
D44V2, continuous
                 vv
clus              DISTANT METASTASIS
  GFRAL MUTATED                    3
  GFRAL WILD-TYPE                  5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  GFRAL MUTATED                                                                                          2
  GFRAL WILD-TYPE                                                                                        7
                 vv
clus              REGIONAL LYMPH NODE
  GFRAL MUTATED                     3
  GFRAL WILD-TYPE                  25
D44V3, multiclass
                                                                                          clus
vv                                                                                         GFRAL MUTATED
  DISTANT METASTASIS                                                                                   3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         GFRAL WILD-TYPE
  DISTANT METASTASIS                                                                                     5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   25
D44V4, binary
                 cls
clus               0  1
  GFRAL MUTATED    4  4
  GFRAL WILD-TYPE 12 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRAL MUTATED      4    4
  GFRAL WILD-TYPE   12   25
        clus
vv       GFRAL MUTATED GFRAL WILD-TYPE
  FEMALE             4              12
  MALE               4              25
                 vv
clus              N0 N1A N1B N2A N2B N3
  GFRAL MUTATED    5   0   0   0   0  2
  GFRAL WILD-TYPE 22   3   4   1   2  3
D44V5, multiclass
D44V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  GFRAL MUTATED             1       0        0        0        0         0
  GFRAL WILD-TYPE           0       3        4        6        4         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  GFRAL MUTATED           2         2         0          0          0
  GFRAL WILD-TYPE         2         0         1          1          6
                 vv
clus              STAGE IIIC STAGE IV
  GFRAL MUTATED            1        1
  GFRAL WILD-TYPE          5        0
D44V7, multiclass

Clustering(45) Variable = ST8SIA3 MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  ST8SIA3 MUTATED    3  1
  ST8SIA3 WILD-TYPE  6 12
  ST8SIA3 MUTATED ST8SIA3 WILD-TYPE 
                4                18 
  ST8SIA3 MUTATED ST8SIA3 WILD-TYPE 
                1                12 
$`ST8SIA3 MUTATED`
TCGA-D3-A3MV TCGA-DA-A1HV TCGA-EE-A185 TCGA-EE-A29S 
        5.39        48.79         4.27         9.99 

$`ST8SIA3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       16.47        28.08         8.38        39.19         7.00        11.57 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
        1.08         8.12         8.84         2.43         8.09        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       23.90         9.67         3.52        42.84        16.21        15.39 

  ST8SIA3 MUTATED ST8SIA3 WILD-TYPE 
             4.27              1.08 
  ST8SIA3 MUTATED ST8SIA3 WILD-TYPE 
            48.79             42.84 
  ST8SIA3 MUTATED ST8SIA3 WILD-TYPE 
             7.69             10.62 
[1] "4.3 - 48.8 (7.7)"  "1.1 - 42.8 (10.6)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE"   "ST8SIA3 MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "ST8SIA3 MUTATED" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "ST8SIA3 MUTATED" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "ST8SIA3 MUTATED" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE"   "ST8SIA3 MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "ST8SIA3 MUTATED" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "ST8SIA3 MUTATED" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "ST8SIA3 MUTATED" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE"   "ST8SIA3 MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "ST8SIA3 MUTATED" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "ST8SIA3 MUTATED" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "ST8SIA3 MUTATED" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"ST8SIA3 WILD-TYPE" "ST8SIA3 WILD-TYPE" 
[1] "hr=" "2.3"
D45V2, continuous
                   vv
clus                DISTANT METASTASIS
  ST8SIA3 MUTATED                    2
  ST8SIA3 WILD-TYPE                  6
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ST8SIA3 MUTATED                                                                                          1
  ST8SIA3 WILD-TYPE                                                                                        8
                   vv
clus                REGIONAL LYMPH NODE
  ST8SIA3 MUTATED                     3
  ST8SIA3 WILD-TYPE                  25
D45V3, multiclass
                                                                                          clus
vv                                                                                         ST8SIA3 MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         ST8SIA3 WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 8
  REGIONAL LYMPH NODE                                                                                     25
D45V4, binary
                   cls
clus                 0  1
  ST8SIA3 MUTATED    4  2
  ST8SIA3 WILD-TYPE 12 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST8SIA3 MUTATED      4    2
  ST8SIA3 WILD-TYPE   12   27
        clus
vv       ST8SIA3 MUTATED ST8SIA3 WILD-TYPE
  FEMALE               4                12
  MALE                 2                27
                   vv
clus                N0 N1A N1B N2A N2B N3
  ST8SIA3 MUTATED    2   0   0   1   1  1
  ST8SIA3 WILD-TYPE 25   3   4   0   1  4
D45V5, multiclass
D45V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ST8SIA3 MUTATED             0       0        0        0        0         1
  ST8SIA3 WILD-TYPE           1       3        4        6        4         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ST8SIA3 MUTATED           0         1         0          0          2
  ST8SIA3 WILD-TYPE         4         1         1          1          4
                   vv
clus                STAGE IIIC STAGE IV
  ST8SIA3 MUTATED            1        0
  ST8SIA3 WILD-TYPE          5        1
D45V7, multiclass

Clustering(46) Variable = DSPP MUTATION ANALYSIS
D46V1, survival
                sevent
clus2             0  1
  DSPP MUTATED    2  0
  DSPP WILD-TYPE  7 13
  DSPP MUTATED DSPP WILD-TYPE 
             2             20 
  DSPP MUTATED DSPP WILD-TYPE 
             0             13 
$`DSPP MUTATED`
TCGA-DA-A1HV TCGA-EE-A29S 
       48.79         9.99 

$`DSPP WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       11.57         4.27         1.08         8.12         8.84         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  DSPP MUTATED DSPP WILD-TYPE 
          9.99           1.08 
  DSPP MUTATED DSPP WILD-TYPE 
         48.79          42.84 
  DSPP MUTATED DSPP WILD-TYPE 
        29.390          9.255 
[1] "10.0 - 48.8 (29.4)" "1.1 - 42.8 (9.3)"  
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "DSPP MUTATED" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
  "DSPP MUTATED" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "DSPP MUTATED" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
  "DSPP MUTATED" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "DSPP MUTATED" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
  "DSPP MUTATED" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" 
[1] "Remove cluster labels:" "DSPP MUTATED"          
clus
  DSPP MUTATED DSPP WILD-TYPE 
             2             20 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X     TCGA-EE-A185 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R     TCGA-EE-A29V 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-EE-A29X     TCGA-EE-A2A1     TCGA-EE-A2A2     TCGA-EE-A2A5 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
    TCGA-ER-A19D     TCGA-ER-A19N     TCGA-GN-A267     TCGA-GN-A268 
"DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" "DSPP WILD-TYPE" 
D46V2, continuous
                vv
clus             DISTANT METASTASIS
  DSPP MUTATED                    0
  DSPP WILD-TYPE                  8
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DSPP MUTATED                                                                                          0
  DSPP WILD-TYPE                                                                                        9
                vv
clus             REGIONAL LYMPH NODE
  DSPP MUTATED                     5
  DSPP WILD-TYPE                  23
D46V3, multiclass
                                                                                          clus
vv                                                                                         DSPP MUTATED
  DISTANT METASTASIS                                                                                  0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            0
  REGIONAL LYMPH NODE                                                                                 5
                                                                                          clus
vv                                                                                         DSPP WILD-TYPE
  DISTANT METASTASIS                                                                                    8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              9
  REGIONAL LYMPH NODE                                                                                  23
D46V4, binary
                cls
clus              0  1
  DSPP MUTATED    2  3
  DSPP WILD-TYPE 14 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSPP MUTATED      2    3
  DSPP WILD-TYPE   14   26
        clus
vv       DSPP MUTATED DSPP WILD-TYPE
  FEMALE            2             14
  MALE              3             26
                vv
clus             N0 N1A N1B N2A N2B N3
  DSPP MUTATED    4   0   0   0   1  0
  DSPP WILD-TYPE 23   3   4   1   1  5
D46V5, multiclass
D46V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DSPP MUTATED             0       1        0        0        2         1
  DSPP WILD-TYPE           1       2        4        6        2         2
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DSPP MUTATED           0         0         0          0          1          0
  DSPP WILD-TYPE         4         2         1          1          5          6
                vv
clus             STAGE IV
  DSPP MUTATED          0
  DSPP WILD-TYPE        1
D46V7, multiclass

Clustering(47) Variable = OR10K2 MUTATION ANALYSIS
D47V1, survival
                  sevent
clus2               0  1
  OR10K2 MUTATED    3  0
  OR10K2 WILD-TYPE  6 13
  OR10K2 MUTATED OR10K2 WILD-TYPE 
               3               19 
  OR10K2 MUTATED OR10K2 WILD-TYPE 
               0               13 
$`OR10K2 MUTATED`
TCGA-DA-A1HV TCGA-EE-A29S TCGA-ER-A19N 
       48.79         9.99        42.84 

$`OR10K2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       11.57         4.27         1.08         8.12         8.84         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A267 
        8.09        25.28        23.90         9.67         3.52        16.21 
TCGA-GN-A268 
       15.39 

  OR10K2 MUTATED OR10K2 WILD-TYPE 
            9.99             1.08 
  OR10K2 MUTATED OR10K2 WILD-TYPE 
           48.79            39.19 
  OR10K2 MUTATED OR10K2 WILD-TYPE 
           42.84             8.84 
[1] "10.0 - 48.8 (42.8)" "1.1 - 39.2 (8.8)"  
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "OR10K2 MUTATED" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "OR10K2 MUTATED" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE"   "OR10K2 MUTATED" 
      TCGA-GN-A267       TCGA-GN-A268 
"OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "OR10K2 MUTATED" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "OR10K2 MUTATED" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE"   "OR10K2 MUTATED" 
      TCGA-GN-A267       TCGA-GN-A268 
"OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "OR10K2 MUTATED" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "OR10K2 MUTATED" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE"   "OR10K2 MUTATED" 
      TCGA-GN-A267       TCGA-GN-A268 
"OR10K2 WILD-TYPE" "OR10K2 WILD-TYPE" 
[1] "hr="   "3e+08"
D47V2, continuous
                  vv
clus               DISTANT METASTASIS
  OR10K2 MUTATED                    1
  OR10K2 WILD-TYPE                  7
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  OR10K2 MUTATED                                                                                          1
  OR10K2 WILD-TYPE                                                                                        8
                  vv
clus               REGIONAL LYMPH NODE
  OR10K2 MUTATED                     5
  OR10K2 WILD-TYPE                  23
D47V3, multiclass
                                                                                          clus
vv                                                                                         OR10K2 MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   5
                                                                                          clus
vv                                                                                         OR10K2 WILD-TYPE
  DISTANT METASTASIS                                                                                      7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    23
D47V4, binary
                  cls
clus                0  1
  OR10K2 MUTATED    2  5
  OR10K2 WILD-TYPE 14 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10K2 MUTATED      2    5
  OR10K2 WILD-TYPE   14   24
        clus
vv       OR10K2 MUTATED OR10K2 WILD-TYPE
  FEMALE              2               14
  MALE                5               24
                  vv
clus               N0 N1A N1B N2A N2B N3
  OR10K2 MUTATED    3   1   0   0   1  0
  OR10K2 WILD-TYPE 24   2   4   1   1  5
D47V5, multiclass
D47V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  OR10K2 MUTATED             0       0        1        0        1         1
  OR10K2 WILD-TYPE           1       3        3        6        3         2
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  OR10K2 MUTATED           0         0         0          0          2
  OR10K2 WILD-TYPE         4         2         1          1          4
                  vv
clus               STAGE IIIC STAGE IV
  OR10K2 MUTATED            0        0
  OR10K2 WILD-TYPE          6        1
D47V7, multiclass

Clustering(48) Variable = CLEC17A MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  CLEC17A MUTATED    2  0
  CLEC17A WILD-TYPE  7 13
  CLEC17A MUTATED CLEC17A WILD-TYPE 
                2                20 
  CLEC17A MUTATED CLEC17A WILD-TYPE 
                0                13 
$`CLEC17A MUTATED`
TCGA-DA-A1HV TCGA-EE-A29S 
       48.79         9.99 

$`CLEC17A WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       11.57         4.27         1.08         8.12         8.84         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  CLEC17A MUTATED CLEC17A WILD-TYPE 
             9.99              1.08 
  CLEC17A MUTATED CLEC17A WILD-TYPE 
            48.79             42.84 
  CLEC17A MUTATED CLEC17A WILD-TYPE 
           29.390             9.255 
[1] "10.0 - 48.8 (29.4)" "1.1 - 42.8 (9.3)"  
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "CLEC17A MUTATED" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "CLEC17A MUTATED" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "CLEC17A MUTATED" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "CLEC17A MUTATED" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "CLEC17A MUTATED" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "CLEC17A MUTATED" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
[1] "Remove cluster labels:" "CLEC17A MUTATED"       
clus
  CLEC17A MUTATED CLEC17A WILD-TYPE 
                2                20 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X        TCGA-EE-A185 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29V 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A5 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19N        TCGA-GN-A267        TCGA-GN-A268 
"CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" "CLEC17A WILD-TYPE" 
D48V2, continuous
                   vv
clus                DISTANT METASTASIS
  CLEC17A MUTATED                    0
  CLEC17A WILD-TYPE                  8
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CLEC17A MUTATED                                                                                          1
  CLEC17A WILD-TYPE                                                                                        8
                   vv
clus                REGIONAL LYMPH NODE
  CLEC17A MUTATED                     2
  CLEC17A WILD-TYPE                  26
D48V3, multiclass
                                                                                          clus
vv                                                                                         CLEC17A MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         CLEC17A WILD-TYPE
  DISTANT METASTASIS                                                                                       8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 8
  REGIONAL LYMPH NODE                                                                                     26
D48V4, binary
                   cls
clus                 0  1
  CLEC17A MUTATED    1  2
  CLEC17A WILD-TYPE 15 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CLEC17A MUTATED      1    2
  CLEC17A WILD-TYPE   15   27
        clus
vv       CLEC17A MUTATED CLEC17A WILD-TYPE
  FEMALE               1                15
  MALE                 2                27
                   vv
clus                N0 N1A N1B N2A N2B N3
  CLEC17A MUTATED    1   1   0   0   1  0
  CLEC17A WILD-TYPE 26   2   4   1   1  5
D48V5, multiclass
D48V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CLEC17A MUTATED             0       0        0        0        0         1
  CLEC17A WILD-TYPE           1       3        4        6        4         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CLEC17A MUTATED           0         0         0          0          2
  CLEC17A WILD-TYPE         4         2         1          1          4
                   vv
clus                STAGE IIIC STAGE IV
  CLEC17A MUTATED            0        0
  CLEC17A WILD-TYPE          6        1
D48V7, multiclass

Clustering(49) Variable = POU6F2 MUTATION ANALYSIS
D49V1, survival
                  sevent
clus2               0  1
  POU6F2 MUTATED    2  2
  POU6F2 WILD-TYPE  7 11
  POU6F2 MUTATED POU6F2 WILD-TYPE 
               4               18 
  POU6F2 MUTATED POU6F2 WILD-TYPE 
               2               11 
$`POU6F2 MUTATED`
TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A2A2 
        1.08         8.84         2.43        23.90 

$`POU6F2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X 
        7.00        11.57         4.27         8.12         9.99         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       25.28         9.67         3.52        42.84        16.21        15.39 

  POU6F2 MUTATED POU6F2 WILD-TYPE 
            1.08             3.52 
  POU6F2 MUTATED POU6F2 WILD-TYPE 
           23.90            48.79 
  POU6F2 MUTATED POU6F2 WILD-TYPE 
           5.635           10.780 
[1] "1.1 - 23.9 (5.6)"  "3.5 - 48.8 (10.8)"
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"POU6F2 WILD-TYPE"   "POU6F2 MUTATED" "POU6F2 WILD-TYPE"   "POU6F2 MUTATED" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"POU6F2 WILD-TYPE"   "POU6F2 MUTATED" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "POU6F2 MUTATED" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"POU6F2 WILD-TYPE"   "POU6F2 MUTATED" "POU6F2 WILD-TYPE"   "POU6F2 MUTATED" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"POU6F2 WILD-TYPE"   "POU6F2 MUTATED" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "POU6F2 MUTATED" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"POU6F2 WILD-TYPE"   "POU6F2 MUTATED" "POU6F2 WILD-TYPE"   "POU6F2 MUTATED" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"POU6F2 WILD-TYPE"   "POU6F2 MUTATED" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "POU6F2 MUTATED" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"POU6F2 WILD-TYPE" "POU6F2 WILD-TYPE" 
[1] "hr=" "1.4"
D49V2, continuous
                  vv
clus               DISTANT METASTASIS
  POU6F2 MUTATED                    1
  POU6F2 WILD-TYPE                  7
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  POU6F2 MUTATED                                                                                          1
  POU6F2 WILD-TYPE                                                                                        8
                  vv
clus               REGIONAL LYMPH NODE
  POU6F2 MUTATED                     6
  POU6F2 WILD-TYPE                  22
D49V3, multiclass
                                                                                          clus
vv                                                                                         POU6F2 MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   6
                                                                                          clus
vv                                                                                         POU6F2 WILD-TYPE
  DISTANT METASTASIS                                                                                      7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    22
D49V4, binary
                  cls
clus                0  1
  POU6F2 MUTATED    3  5
  POU6F2 WILD-TYPE 13 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POU6F2 MUTATED      3    5
  POU6F2 WILD-TYPE   13   24
        clus
vv       POU6F2 MUTATED POU6F2 WILD-TYPE
  FEMALE              3               13
  MALE                5               24
                  vv
clus               N0 N1A N1B N2A N2B N3
  POU6F2 MUTATED    4   0   3   0   0  1
  POU6F2 WILD-TYPE 23   3   1   1   2  4
D49V5, multiclass
D49V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  POU6F2 MUTATED             0       1        2        0        0         1
  POU6F2 WILD-TYPE           1       2        2        6        4         2
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  POU6F2 MUTATED           0         0         0          0          1
  POU6F2 WILD-TYPE         4         2         1          1          5
                  vv
clus               STAGE IIIC STAGE IV
  POU6F2 MUTATED            3        0
  POU6F2 WILD-TYPE          3        1
D49V7, multiclass

Clustering(50) Variable = LRRIQ3 MUTATION ANALYSIS
D50V1, survival
                  sevent
clus2               0  1
  LRRIQ3 MUTATED    2  2
  LRRIQ3 WILD-TYPE  7 11
  LRRIQ3 MUTATED LRRIQ3 WILD-TYPE 
               4               18 
  LRRIQ3 MUTATED LRRIQ3 WILD-TYPE 
               2               11 
$`LRRIQ3 MUTATED`
TCGA-D3-A1Q1 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A29V 
       16.47        48.79        39.19         2.43 

$`LRRIQ3 WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 
       28.08         8.38         5.39         7.00        11.57         4.27 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A1 
        1.08         8.12         8.84         9.99         8.09        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       23.90         9.67         3.52        42.84        16.21        15.39 

  LRRIQ3 MUTATED LRRIQ3 WILD-TYPE 
            2.43             1.08 
  LRRIQ3 MUTATED LRRIQ3 WILD-TYPE 
           48.79            42.84 
  LRRIQ3 MUTATED LRRIQ3 WILD-TYPE 
          27.830            9.255 
[1] "2.4 - 48.8 (27.8)" "1.1 - 42.8 (9.3)" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
  "LRRIQ3 MUTATED" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "LRRIQ3 MUTATED"   "LRRIQ3 MUTATED" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"LRRIQ3 WILD-TYPE"   "LRRIQ3 MUTATED" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
  "LRRIQ3 MUTATED" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "LRRIQ3 MUTATED"   "LRRIQ3 MUTATED" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"LRRIQ3 WILD-TYPE"   "LRRIQ3 MUTATED" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
  "LRRIQ3 MUTATED" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "LRRIQ3 MUTATED"   "LRRIQ3 MUTATED" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"LRRIQ3 WILD-TYPE"   "LRRIQ3 MUTATED" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"LRRIQ3 WILD-TYPE" "LRRIQ3 WILD-TYPE" 
[1] "hr=" "2.1"
D50V2, continuous
                  vv
clus               DISTANT METASTASIS
  LRRIQ3 MUTATED                    1
  LRRIQ3 WILD-TYPE                  7
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  LRRIQ3 MUTATED                                                                                          1
  LRRIQ3 WILD-TYPE                                                                                        8
                  vv
clus               REGIONAL LYMPH NODE
  LRRIQ3 MUTATED                     5
  LRRIQ3 WILD-TYPE                  23
D50V3, multiclass
                                                                                          clus
vv                                                                                         LRRIQ3 MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   5
                                                                                          clus
vv                                                                                         LRRIQ3 WILD-TYPE
  DISTANT METASTASIS                                                                                      7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    23
D50V4, binary
                  cls
clus                0  1
  LRRIQ3 MUTATED    2  5
  LRRIQ3 WILD-TYPE 14 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRIQ3 MUTATED      2    5
  LRRIQ3 WILD-TYPE   14   24
        clus
vv       LRRIQ3 MUTATED LRRIQ3 WILD-TYPE
  FEMALE              2               14
  MALE                5               24
                  vv
clus               N0 N1A N1B N2A N2B N3
  LRRIQ3 MUTATED    2   0   1   0   1  2
  LRRIQ3 WILD-TYPE 25   3   3   1   1  3
D50V5, multiclass
D50V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  LRRIQ3 MUTATED             0       1        0        0        1         0
  LRRIQ3 WILD-TYPE           1       2        4        6        3         3
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  LRRIQ3 MUTATED           0         0         0          0          1
  LRRIQ3 WILD-TYPE         4         2         1          1          5
                  vv
clus               STAGE IIIC STAGE IV
  LRRIQ3 MUTATED            3        0
  LRRIQ3 WILD-TYPE          3        1
D50V7, multiclass

Clustering(51) Variable = ARID2 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2              0  1
  ARID2 MUTATED    2  0
  ARID2 WILD-TYPE  7 13
  ARID2 MUTATED ARID2 WILD-TYPE 
              2              20 
  ARID2 MUTATED ARID2 WILD-TYPE 
              0              13 
$`ARID2 MUTATED`
TCGA-EE-A29S TCGA-EE-A2A2 
        9.99        23.90 

$`ARID2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
        7.00        11.57         4.27         1.08         8.12         8.84 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        2.43         8.09        25.28         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  ARID2 MUTATED ARID2 WILD-TYPE 
           9.99            1.08 
  ARID2 MUTATED ARID2 WILD-TYPE 
          23.90           48.79 
  ARID2 MUTATED ARID2 WILD-TYPE 
         16.945           9.255 
[1] "10.0 - 23.9 (16.9)" "1.1 - 48.8 (9.3)"  
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "ARID2 MUTATED" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "ARID2 MUTATED" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "ARID2 MUTATED" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "ARID2 MUTATED" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "ARID2 MUTATED" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "ARID2 MUTATED" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
[1] "Remove cluster labels:" "ARID2 MUTATED"         
clus
  ARID2 MUTATED ARID2 WILD-TYPE 
              2              20 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1      TCGA-EE-A2A5 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-ER-A19D      TCGA-ER-A19N      TCGA-GN-A267      TCGA-GN-A268 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
D51V2, continuous
                 vv
clus              DISTANT METASTASIS
  ARID2 MUTATED                    1
  ARID2 WILD-TYPE                  7
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ARID2 MUTATED                                                                                          1
  ARID2 WILD-TYPE                                                                                        8
                 vv
clus              REGIONAL LYMPH NODE
  ARID2 MUTATED                     7
  ARID2 WILD-TYPE                  21
D51V3, multiclass
                                                                                          clus
vv                                                                                         ARID2 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  7
                                                                                          clus
vv                                                                                         ARID2 WILD-TYPE
  DISTANT METASTASIS                                                                                     7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               8
  REGIONAL LYMPH NODE                                                                                   21
D51V4, binary
                 cls
clus               0  1
  ARID2 MUTATED    2  7
  ARID2 WILD-TYPE 14 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      2    7
  ARID2 WILD-TYPE   14   22
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  FEMALE             2              14
  MALE               7              22
                 vv
clus              N0 N1A N1B N2A N2B N3
  ARID2 MUTATED    6   0   1   0   0  0
  ARID2 WILD-TYPE 21   3   3   1   2  5
D51V5, multiclass
D51V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ARID2 MUTATED             0       1        1        0        2         1
  ARID2 WILD-TYPE           1       2        3        6        2         2
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ARID2 MUTATED           1         0         0          0          1
  ARID2 WILD-TYPE         3         2         1          1          5
                 vv
clus              STAGE IIIC STAGE IV
  ARID2 MUTATED            0        0
  ARID2 WILD-TYPE          6        1
D51V7, multiclass

Clustering(52) Variable = GAS2 MUTATION ANALYSIS
D52V1, survival
                sevent
clus2             0  1
  GAS2 WILD-TYPE  9 13
GAS2 WILD-TYPE 
            22 
[1] 13
$`GAS2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
        7.00        11.57         4.27         1.08         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        9.99         2.43         8.09        25.28        23.90         9.67 
TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
        3.52        42.84        16.21        15.39 

GAS2 WILD-TYPE 
          1.08 
GAS2 WILD-TYPE 
         48.79 
GAS2 WILD-TYPE 
          9.83 
[1] "1.1 - 48.8 (9.8)"
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"GAS2 WILD-TYPE" "GAS2 WILD-TYPE" 
D52V2, continuous
                vv
clus             DISTANT METASTASIS
  GAS2 MUTATED                    2
  GAS2 WILD-TYPE                  6
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  GAS2 MUTATED                                                                                          1
  GAS2 WILD-TYPE                                                                                        8
                vv
clus             REGIONAL LYMPH NODE
  GAS2 MUTATED                     2
  GAS2 WILD-TYPE                  26
D52V3, multiclass
                                                                                          clus
vv                                                                                         GAS2 MUTATED
  DISTANT METASTASIS                                                                                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            1
  REGIONAL LYMPH NODE                                                                                 2
                                                                                          clus
vv                                                                                         GAS2 WILD-TYPE
  DISTANT METASTASIS                                                                                    6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              8
  REGIONAL LYMPH NODE                                                                                  26
D52V4, binary
                cls
clus              0  1
  GAS2 MUTATED    1  4
  GAS2 WILD-TYPE 15 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAS2 MUTATED      1    4
  GAS2 WILD-TYPE   15   25
        clus
vv       GAS2 MUTATED GAS2 WILD-TYPE
  FEMALE            1             15
  MALE              4             25
                vv
clus             N0 N1A N1B N2A N2B N3
  GAS2 MUTATED    4   1   0   0   0  0
  GAS2 WILD-TYPE 23   2   4   1   2  5
D52V5, multiclass
D52V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  GAS2 MUTATED             0       0        2        0        2         0
  GAS2 WILD-TYPE           1       3        2        6        2         3
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  GAS2 MUTATED           0         0         0          0          1          0
  GAS2 WILD-TYPE         4         2         1          1          5          6
                vv
clus             STAGE IV
  GAS2 MUTATED          0
  GAS2 WILD-TYPE        1
D52V7, multiclass

Clustering(53) Variable = SIRPB1 MUTATION ANALYSIS
D53V1, survival
                  sevent
clus2               0  1
  SIRPB1 MUTATED    2  2
  SIRPB1 WILD-TYPE  7 11
  SIRPB1 MUTATED SIRPB1 WILD-TYPE 
               4               18 
  SIRPB1 MUTATED SIRPB1 WILD-TYPE 
               2               11 
$`SIRPB1 MUTATED`
TCGA-D3-A2J8 TCGA-EE-A29L TCGA-EE-A29Q TCGA-ER-A19N 
        8.38         1.08         8.12        42.84 

$`SIRPB1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       11.57         4.27         8.84         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A267 TCGA-GN-A268 
       25.28        23.90         9.67         3.52        16.21        15.39 

  SIRPB1 MUTATED SIRPB1 WILD-TYPE 
            1.08             2.43 
  SIRPB1 MUTATED SIRPB1 WILD-TYPE 
           42.84            48.79 
  SIRPB1 MUTATED SIRPB1 WILD-TYPE 
            8.25            10.78 
[1] "1.1 - 42.8 (8.2)"  "2.4 - 48.8 (10.8)"
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE"   "SIRPB1 MUTATED" "SIRPB1 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"SIRPB1 WILD-TYPE"   "SIRPB1 MUTATED"   "SIRPB1 MUTATED" "SIRPB1 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE"   "SIRPB1 MUTATED" 
      TCGA-GN-A267       TCGA-GN-A268 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE"   "SIRPB1 MUTATED" "SIRPB1 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"SIRPB1 WILD-TYPE"   "SIRPB1 MUTATED"   "SIRPB1 MUTATED" "SIRPB1 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE"   "SIRPB1 MUTATED" 
      TCGA-GN-A267       TCGA-GN-A268 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE"   "SIRPB1 MUTATED" "SIRPB1 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"SIRPB1 WILD-TYPE"   "SIRPB1 MUTATED"   "SIRPB1 MUTATED" "SIRPB1 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE"   "SIRPB1 MUTATED" 
      TCGA-GN-A267       TCGA-GN-A268 
"SIRPB1 WILD-TYPE" "SIRPB1 WILD-TYPE" 
[1] "hr=" "1"  
D53V2, continuous
                  vv
clus               DISTANT METASTASIS
  SIRPB1 MUTATED                    0
  SIRPB1 WILD-TYPE                  8
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  SIRPB1 MUTATED                                                                                          1
  SIRPB1 WILD-TYPE                                                                                        8
                  vv
clus               REGIONAL LYMPH NODE
  SIRPB1 MUTATED                     5
  SIRPB1 WILD-TYPE                  23
D53V3, 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                                                                                      8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    23
D53V4, binary
                  cls
clus                0  1
  SIRPB1 MUTATED    1  5
  SIRPB1 WILD-TYPE 15 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SIRPB1 MUTATED      1    5
  SIRPB1 WILD-TYPE   15   24
        clus
vv       SIRPB1 MUTATED SIRPB1 WILD-TYPE
  FEMALE              1               15
  MALE                5               24
                  vv
clus               N0 N1A N1B N2A N2B N3
  SIRPB1 MUTATED    3   1   0   0   0  1
  SIRPB1 WILD-TYPE 24   2   4   1   2  4
D53V5, multiclass
D53V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  SIRPB1 MUTATED             0       0        0        1        1         0
  SIRPB1 WILD-TYPE           1       3        4        5        3         3
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  SIRPB1 MUTATED           1         0         0          0          1
  SIRPB1 WILD-TYPE         3         2         1          1          5
                  vv
clus               STAGE IIIC STAGE IV
  SIRPB1 MUTATED            1        0
  SIRPB1 WILD-TYPE          5        1
D53V7, multiclass

Clustering(54) Variable = ACTC1 MUTATION ANALYSIS
D54V1, survival
                 sevent
clus2              0  1
  ACTC1 MUTATED    1  1
  ACTC1 WILD-TYPE  8 12
  ACTC1 MUTATED ACTC1 WILD-TYPE 
              2              20 
  ACTC1 MUTATED ACTC1 WILD-TYPE 
              1              12 
$`ACTC1 MUTATED`
TCGA-EE-A29L TCGA-EE-A29S 
        1.08         9.99 

$`ACTC1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
        7.00        11.57         4.27         8.12         8.84         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  ACTC1 MUTATED ACTC1 WILD-TYPE 
           1.08            2.43 
  ACTC1 MUTATED ACTC1 WILD-TYPE 
           9.99           48.79 
  ACTC1 MUTATED ACTC1 WILD-TYPE 
          5.535          10.620 
[1] "1.1 - 10.0 (5.5)"  "2.4 - 48.8 (10.6)"
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ACTC1 WILD-TYPE"   "ACTC1 MUTATED" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "ACTC1 MUTATED" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ACTC1 WILD-TYPE"   "ACTC1 MUTATED" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "ACTC1 MUTATED" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ACTC1 WILD-TYPE"   "ACTC1 MUTATED" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "ACTC1 MUTATED" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
[1] "Remove cluster labels:" "ACTC1 MUTATED"         
clus
  ACTC1 MUTATED ACTC1 WILD-TYPE 
              2              20 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29Q      TCGA-EE-A29R      TCGA-EE-A29V 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-EE-A29X      TCGA-EE-A2A1      TCGA-EE-A2A2      TCGA-EE-A2A5 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
     TCGA-ER-A19D      TCGA-ER-A19N      TCGA-GN-A267      TCGA-GN-A268 
"ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" "ACTC1 WILD-TYPE" 
D54V2, continuous
                 vv
clus              DISTANT METASTASIS
  ACTC1 MUTATED                    1
  ACTC1 WILD-TYPE                  7
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ACTC1 MUTATED                                                                                          0
  ACTC1 WILD-TYPE                                                                                        9
                 vv
clus              REGIONAL LYMPH NODE
  ACTC1 MUTATED                     3
  ACTC1 WILD-TYPE                  25
D54V3, multiclass
                                                                                          clus
vv                                                                                         ACTC1 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         ACTC1 WILD-TYPE
  DISTANT METASTASIS                                                                                     7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               9
  REGIONAL LYMPH NODE                                                                                   25
D54V4, binary
                 cls
clus               0  1
  ACTC1 MUTATED    0  4
  ACTC1 WILD-TYPE 16 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTC1 MUTATED      0    4
  ACTC1 WILD-TYPE   16   25
        clus
vv       ACTC1 MUTATED ACTC1 WILD-TYPE
  FEMALE             0              16
  MALE               4              25
                 vv
clus              N0 N1A N1B N2A N2B N3
  ACTC1 MUTATED    2   0   1   0   0  1
  ACTC1 WILD-TYPE 25   3   3   1   2  4
D54V5, multiclass
D54V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ACTC1 MUTATED             0       0        0        0        1         1
  ACTC1 WILD-TYPE           1       3        4        6        3         2
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ACTC1 MUTATED           0         0         1          0          0
  ACTC1 WILD-TYPE         4         2         0          1          6
                 vv
clus              STAGE IIIC STAGE IV
  ACTC1 MUTATED            1        0
  ACTC1 WILD-TYPE          5        1
D54V7, multiclass

Clustering(55) Variable = PRB2 MUTATION ANALYSIS
D55V1, survival
                sevent
clus2             0  1
  PRB2 MUTATED    1  2
  PRB2 WILD-TYPE  8 11
  PRB2 MUTATED PRB2 WILD-TYPE 
             3             19 
  PRB2 MUTATED PRB2 WILD-TYPE 
             2             11 
$`PRB2 MUTATED`
TCGA-DA-A3F3 TCGA-EE-A29S TCGA-EE-A29V 
        7.00         9.99         2.43 

$`PRB2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29X 
       11.57         4.27         1.08         8.12         8.84         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
       25.28        23.90         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  PRB2 MUTATED PRB2 WILD-TYPE 
          2.43           1.08 
  PRB2 MUTATED PRB2 WILD-TYPE 
          9.99          48.79 
  PRB2 MUTATED PRB2 WILD-TYPE 
          7.00          11.57 
[1] "2.4 - 10.0 (7.0)"  "1.1 - 48.8 (11.6)"
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE"   "PRB2 MUTATED" "PRB2 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
  "PRB2 MUTATED"   "PRB2 MUTATED" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE"   "PRB2 MUTATED" "PRB2 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
  "PRB2 MUTATED"   "PRB2 MUTATED" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE"   "PRB2 MUTATED" "PRB2 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
  "PRB2 MUTATED"   "PRB2 MUTATED" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
[1] "hr=" "3"  
D55V2, continuous
                vv
clus             DISTANT METASTASIS
  PRB2 MUTATED                    1
  PRB2 WILD-TYPE                  7
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  PRB2 MUTATED                                                                                          0
  PRB2 WILD-TYPE                                                                                        9
                vv
clus             REGIONAL LYMPH NODE
  PRB2 MUTATED                     4
  PRB2 WILD-TYPE                  24
D55V3, multiclass
                                                                                          clus
vv                                                                                         PRB2 MUTATED
  DISTANT METASTASIS                                                                                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            0
  REGIONAL LYMPH NODE                                                                                 4
                                                                                          clus
vv                                                                                         PRB2 WILD-TYPE
  DISTANT METASTASIS                                                                                    7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              9
  REGIONAL LYMPH NODE                                                                                  24
D55V4, binary
                cls
clus              0  1
  PRB2 MUTATED    0  5
  PRB2 WILD-TYPE 16 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      0    5
  PRB2 WILD-TYPE   16   24
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  FEMALE            0             16
  MALE              5             24
                vv
clus             N0 N1A N1B N2A N2B N3
  PRB2 MUTATED    2   0   1   0   1  0
  PRB2 WILD-TYPE 25   3   3   1   1  5
D55V5, multiclass
D55V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  PRB2 MUTATED             0       0        1        0        0         1
  PRB2 WILD-TYPE           1       3        3        6        4         2
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PRB2 MUTATED           0         0         0          0          1          1
  PRB2 WILD-TYPE         4         2         1          1          5          5
                vv
clus             STAGE IV
  PRB2 MUTATED          0
  PRB2 WILD-TYPE        1
D55V7, multiclass

Clustering(56) Variable = C15ORF23 MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                 0  1
  C15ORF23 MUTATED    1  0
  C15ORF23 WILD-TYPE  8 13
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                 1                 21 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                 0                 13 
$`C15ORF23 MUTATED`
TCGA-EE-A2A2 
        23.9 

$`C15ORF23 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
        7.00        11.57         4.27         1.08         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D 
        9.99         2.43         8.09        25.28         9.67         3.52 
TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       42.84        16.21        15.39 

  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
             23.90               1.08 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
             23.90              48.79 
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
             23.90               9.67 
[1] "23.9 - 23.9 (23.9)" "1.1 - 48.8 (9.7)"  
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"C15ORF23 WILD-TYPE"   "C15ORF23 MUTATED" "C15ORF23 WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-GN-A268 
"C15ORF23 WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"C15ORF23 WILD-TYPE"   "C15ORF23 MUTATED" "C15ORF23 WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-GN-A268 
"C15ORF23 WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"C15ORF23 WILD-TYPE"   "C15ORF23 MUTATED" "C15ORF23 WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-GN-A268 
"C15ORF23 WILD-TYPE" 
[1] "Remove cluster labels:" "C15ORF23 MUTATED"      
clus
  C15ORF23 MUTATED C15ORF23 WILD-TYPE 
                 1                 21 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A5         TCGA-ER-A19D 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
        TCGA-ER-A19N         TCGA-GN-A267         TCGA-GN-A268 
"C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" "C15ORF23 WILD-TYPE" 
D56V2, continuous
                    vv
clus                 DISTANT METASTASIS
  C15ORF23 MUTATED                    1
  C15ORF23 WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  C15ORF23 MUTATED                                                                                          1
  C15ORF23 WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  C15ORF23 MUTATED                     1
  C15ORF23 WILD-TYPE                  27
D56V3, multiclass
                                                                                          clus
vv                                                                                         C15ORF23 MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     1
                                                                                          clus
vv                                                                                         C15ORF23 WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      27
D56V4, binary
                    cls
clus                  0  1
  C15ORF23 MUTATED    1  2
  C15ORF23 WILD-TYPE 15 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF23 MUTATED      1    2
  C15ORF23 WILD-TYPE   15   27
        clus
vv       C15ORF23 MUTATED C15ORF23 WILD-TYPE
  FEMALE                1                 15
  MALE                  2                 27
                    vv
clus                 N0 N1A N1B N2A N2B N3
  C15ORF23 MUTATED    1   0   2   0   0  0
  C15ORF23 WILD-TYPE 26   3   2   1   2  5
D56V5, multiclass
D56V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  C15ORF23 MUTATED             0       0        0        0        0         0
  C15ORF23 WILD-TYPE           1       3        4        6        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  C15ORF23 MUTATED           1         0         1          0          1
  C15ORF23 WILD-TYPE         3         2         0          1          5
                    vv
clus                 STAGE IIIC STAGE IV
  C15ORF23 MUTATED            0        0
  C15ORF23 WILD-TYPE          6        1
D56V7, multiclass

Clustering(57) Variable = FASLG MUTATION ANALYSIS
D57V1, survival
                 sevent
clus2              0  1
  FASLG MUTATED    0  1
  FASLG WILD-TYPE  9 12
  FASLG MUTATED FASLG WILD-TYPE 
              1              21 
  FASLG MUTATED FASLG WILD-TYPE 
              1              12 
$`FASLG MUTATED`
TCGA-EE-A17X 
       11.57 

$`FASLG WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        7.00         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        2.43         8.09        25.28        23.90         9.67         3.52 
TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       42.84        16.21        15.39 

  FASLG MUTATED FASLG WILD-TYPE 
          11.57            1.08 
  FASLG MUTATED FASLG WILD-TYPE 
          11.57           48.79 
  FASLG MUTATED FASLG WILD-TYPE 
          11.57            9.67 
[1] "11.6 - 11.6 (11.6)" "1.1 - 48.8 (9.7)"  
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE"   "FASLG MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE"   "FASLG MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE"   "FASLG MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" 
[1] "Remove cluster labels:" "FASLG MUTATED"         
clus
  FASLG MUTATED FASLG WILD-TYPE 
              1              21 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A185 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R      TCGA-EE-A29S 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1      TCGA-EE-A2A2 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N      TCGA-GN-A267 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-GN-A268 
"FASLG WILD-TYPE" 
D57V2, continuous
                 vv
clus              DISTANT METASTASIS
  FASLG MUTATED                    0
  FASLG WILD-TYPE                  8
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  FASLG MUTATED                                                                                          0
  FASLG WILD-TYPE                                                                                        9
                 vv
clus              REGIONAL LYMPH NODE
  FASLG MUTATED                     3
  FASLG WILD-TYPE                  25
D57V3, multiclass
                                                                                          clus
vv                                                                                         FASLG MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         FASLG WILD-TYPE
  DISTANT METASTASIS                                                                                     8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               9
  REGIONAL LYMPH NODE                                                                                   25
D57V4, binary
                 cls
clus               0  1
  FASLG MUTATED    1  2
  FASLG WILD-TYPE 15 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FASLG MUTATED      1    2
  FASLG WILD-TYPE   15   27
        clus
vv       FASLG MUTATED FASLG WILD-TYPE
  FEMALE             1              15
  MALE               2              27
                 vv
clus              N0 N1A N1B N2A N2B N3
  FASLG MUTATED    2   0   0   0   0  0
  FASLG WILD-TYPE 25   3   4   1   2  5
D57V5, multiclass
[1] "Remove cluster labels:" "FASLG MUTATED"         
clus
  FASLG MUTATED FASLG WILD-TYPE 
              2              40 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A185 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R      TCGA-EE-A29S 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1      TCGA-EE-A2A2 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A2A5      TCGA-EE-A2GD      TCGA-EE-A2GJ      TCGA-EE-A2GL 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A2GM      TCGA-EE-A2GN      TCGA-EE-A2GP      TCGA-EE-A2GU 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A2MC      TCGA-EE-A2MD      TCGA-EE-A2ML      TCGA-EE-A2MN 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-ER-A19D      TCGA-FS-A1YW      TCGA-FS-A1Z0      TCGA-FS-A1ZB 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-FS-A1ZE      TCGA-FS-A1ZP      TCGA-FS-A1ZQ      TCGA-FS-A1ZT 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-FS-A1ZW      TCGA-FS-A1ZY      TCGA-GN-A267      TCGA-GN-A268 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
D57V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  FASLG MUTATED             0       1        1        0        0         0
  FASLG WILD-TYPE           1       2        3        6        4         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  FASLG MUTATED           0         0         0          0          0
  FASLG WILD-TYPE         4         2         1          1          6
                 vv
clus              STAGE IIIC STAGE IV
  FASLG MUTATED            0        0
  FASLG WILD-TYPE          6        1
D57V7, multiclass
[1] "Remove cluster labels:" "FASLG MUTATED"         
clus
  FASLG MUTATED FASLG WILD-TYPE 
              2              40 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A185 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R      TCGA-EE-A29S 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1      TCGA-EE-A2A2 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A2A5      TCGA-EE-A2GD      TCGA-EE-A2GJ      TCGA-EE-A2GL 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A2GM      TCGA-EE-A2GN      TCGA-EE-A2GP      TCGA-EE-A2GU 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-EE-A2MC      TCGA-EE-A2MD      TCGA-EE-A2ML      TCGA-EE-A2MN 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-ER-A19D      TCGA-FS-A1YW      TCGA-FS-A1Z0      TCGA-FS-A1ZB 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-FS-A1ZE      TCGA-FS-A1ZP      TCGA-FS-A1ZQ      TCGA-FS-A1ZT 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 
     TCGA-FS-A1ZW      TCGA-FS-A1ZY      TCGA-GN-A267      TCGA-GN-A268 
"FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" "FASLG WILD-TYPE" 

Clustering(58) Variable = PAK7 MUTATION ANALYSIS
D58V1, survival
                sevent
clus2             0  1
  PAK7 MUTATED    2  1
  PAK7 WILD-TYPE  7 12
  PAK7 MUTATED PAK7 WILD-TYPE 
             3             19 
  PAK7 MUTATED PAK7 WILD-TYPE 
             1             12 
$`PAK7 MUTATED`
TCGA-D3-A3MV TCGA-DA-A1HV TCGA-EE-A29L 
        5.39        48.79         1.08 

$`PAK7 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       16.47        28.08         8.38        39.19         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
        4.27         8.12         8.84         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
       25.28        23.90         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  PAK7 MUTATED PAK7 WILD-TYPE 
          1.08           2.43 
  PAK7 MUTATED PAK7 WILD-TYPE 
         48.79          42.84 
  PAK7 MUTATED PAK7 WILD-TYPE 
          5.39           9.99 
[1] "1.1 - 48.8 (5.4)"  "2.4 - 42.8 (10.0)"
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE"   "PAK7 MUTATED" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "PAK7 MUTATED" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"PAK7 WILD-TYPE"   "PAK7 MUTATED" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"PAK7 WILD-TYPE" "PAK7 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE"   "PAK7 MUTATED" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "PAK7 MUTATED" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"PAK7 WILD-TYPE"   "PAK7 MUTATED" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"PAK7 WILD-TYPE" "PAK7 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE"   "PAK7 MUTATED" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "PAK7 MUTATED" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"PAK7 WILD-TYPE"   "PAK7 MUTATED" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" "PAK7 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"PAK7 WILD-TYPE" "PAK7 WILD-TYPE" 
[1] "hr=" "1.5"
D58V2, continuous
                vv
clus             DISTANT METASTASIS
  PAK7 MUTATED                    1
  PAK7 WILD-TYPE                  7
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  PAK7 MUTATED                                                                                          1
  PAK7 WILD-TYPE                                                                                        8
                vv
clus             REGIONAL LYMPH NODE
  PAK7 MUTATED                     7
  PAK7 WILD-TYPE                  21
D58V3, multiclass
                                                                                          clus
vv                                                                                         PAK7 MUTATED
  DISTANT METASTASIS                                                                                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            1
  REGIONAL LYMPH NODE                                                                                 7
                                                                                          clus
vv                                                                                         PAK7 WILD-TYPE
  DISTANT METASTASIS                                                                                    7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              8
  REGIONAL LYMPH NODE                                                                                  21
D58V4, binary
                cls
clus              0  1
  PAK7 MUTATED    3  6
  PAK7 WILD-TYPE 13 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK7 MUTATED      3    6
  PAK7 WILD-TYPE   13   23
        clus
vv       PAK7 MUTATED PAK7 WILD-TYPE
  FEMALE            3             13
  MALE              6             23
                vv
clus             N0 N1A N1B N2A N2B N3
  PAK7 MUTATED    4   1   0   1   1  1
  PAK7 WILD-TYPE 23   2   4   0   1  4
D58V5, multiclass
D58V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  PAK7 MUTATED             0       1        1        0        2         0
  PAK7 WILD-TYPE           1       2        3        6        2         3
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PAK7 MUTATED           0         0         0          0          3          1
  PAK7 WILD-TYPE         4         2         1          1          3          5
                vv
clus             STAGE IV
  PAK7 MUTATED          0
  PAK7 WILD-TYPE        1
D58V7, multiclass

Clustering(59) Variable = SIGLEC14 MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  SIGLEC14 MUTATED    1  1
  SIGLEC14 WILD-TYPE  8 12
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 2                 20 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 1                 12 
$`SIGLEC14 MUTATED`
TCGA-DA-A1I1 TCGA-EE-A29V 
       39.19         2.43 

$`SIGLEC14 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        48.79         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
              2.43               1.08 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
             39.19              48.79 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
             20.81               9.83 
[1] "2.4 - 39.2 (20.8)" "1.1 - 48.8 (9.8)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE"   "SIGLEC14 MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"SIGLEC14 WILD-TYPE"   "SIGLEC14 MUTATED" "SIGLEC14 WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-GN-A268 
"SIGLEC14 WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE"   "SIGLEC14 MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"SIGLEC14 WILD-TYPE"   "SIGLEC14 MUTATED" "SIGLEC14 WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-GN-A268 
"SIGLEC14 WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE"   "SIGLEC14 MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"SIGLEC14 WILD-TYPE"   "SIGLEC14 MUTATED" "SIGLEC14 WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-GN-A268 
"SIGLEC14 WILD-TYPE" 
[1] "Remove cluster labels:" "SIGLEC14 MUTATED"      
clus
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 2                 20 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A3F3 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A185         TCGA-EE-A29L 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A1         TCGA-EE-A2A2 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-EE-A2A5         TCGA-ER-A19D         TCGA-ER-A19N 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
D59V2, continuous
                    vv
clus                 DISTANT METASTASIS
  SIGLEC14 MUTATED                    2
  SIGLEC14 WILD-TYPE                  6
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  SIGLEC14 MUTATED                                                                                          1
  SIGLEC14 WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  SIGLEC14 MUTATED                     0
  SIGLEC14 WILD-TYPE                  28
D59V3, multiclass
                                                                                          clus
vv                                                                                         SIGLEC14 MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     0
                                                                                          clus
vv                                                                                         SIGLEC14 WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      28
D59V4, binary
                    cls
clus                  0  1
  SIGLEC14 MUTATED    0  3
  SIGLEC14 WILD-TYPE 16 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      0    3
  SIGLEC14 WILD-TYPE   16   26
        clus
vv       SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  FEMALE                0                 16
  MALE                  3                 26
                    vv
clus                 N0 N1A N1B N2A N2B N3
  SIGLEC14 MUTATED    1   0   1   0   0  1
  SIGLEC14 WILD-TYPE 26   3   3   1   2  4
D59V5, multiclass
D59V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  SIGLEC14 MUTATED             0       0        0        0        0         0
  SIGLEC14 WILD-TYPE           1       3        4        6        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  SIGLEC14 MUTATED           1         0         0          0          0
  SIGLEC14 WILD-TYPE         3         2         1          1          6
                    vv
clus                 STAGE IIIC STAGE IV
  SIGLEC14 MUTATED            2        0
  SIGLEC14 WILD-TYPE          4        1
D59V7, multiclass

Clustering(60) Variable = TPTE2 MUTATION ANALYSIS
D60V1, survival
                 sevent
clus2              0  1
  TPTE2 MUTATED    1  2
  TPTE2 WILD-TYPE  8 11
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              3              19 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              2              11 
$`TPTE2 MUTATED`
TCGA-DA-A1I1 TCGA-EE-A17X TCGA-EE-A29V 
       39.19        11.57         2.43 

$`TPTE2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        48.79         7.00 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X 
        4.27         1.08         8.12         8.84         9.99         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
       25.28        23.90         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  TPTE2 MUTATED TPTE2 WILD-TYPE 
           2.43            1.08 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
          39.19           48.79 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
          11.57            9.67 
[1] "2.4 - 39.2 (11.6)" "1.1 - 48.8 (9.7)" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"TPTE2 WILD-TYPE"   "TPTE2 MUTATED" "TPTE2 WILD-TYPE"   "TPTE2 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"TPTE2 WILD-TYPE"   "TPTE2 MUTATED" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"TPTE2 WILD-TYPE"   "TPTE2 MUTATED" "TPTE2 WILD-TYPE"   "TPTE2 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"TPTE2 WILD-TYPE"   "TPTE2 MUTATED" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"TPTE2 WILD-TYPE"   "TPTE2 MUTATED" "TPTE2 WILD-TYPE"   "TPTE2 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"TPTE2 WILD-TYPE"   "TPTE2 MUTATED" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"TPTE2 WILD-TYPE" "TPTE2 WILD-TYPE" 
[1] "hr=" "1.1"
D60V2, continuous
                 vv
clus              DISTANT METASTASIS
  TPTE2 MUTATED                    2
  TPTE2 WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  TPTE2 MUTATED                                                                                          1
  TPTE2 WILD-TYPE                                                                                        8
                 vv
clus              REGIONAL LYMPH NODE
  TPTE2 MUTATED                     3
  TPTE2 WILD-TYPE                  25
D60V3, multiclass
                                                                                          clus
vv                                                                                         TPTE2 MUTATED
  DISTANT METASTASIS                                                                                   2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         TPTE2 WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               8
  REGIONAL LYMPH NODE                                                                                   25
D60V4, binary
                 cls
clus               0  1
  TPTE2 MUTATED    1  5
  TPTE2 WILD-TYPE 15 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      1    5
  TPTE2 WILD-TYPE   15   24
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  FEMALE             1              15
  MALE               5              24
                 vv
clus              N0 N1A N1B N2A N2B N3
  TPTE2 MUTATED    2   0   1   0   0  1
  TPTE2 WILD-TYPE 25   3   3   1   2  4
D60V5, multiclass
D60V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  TPTE2 MUTATED             0       0        1        0        1         0
  TPTE2 WILD-TYPE           1       3        3        6        3         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  TPTE2 MUTATED           0         0         0          0          0
  TPTE2 WILD-TYPE         4         2         1          1          6
                 vv
clus              STAGE IIIC STAGE IV
  TPTE2 MUTATED            2        0
  TPTE2 WILD-TYPE          4        1
D60V7, multiclass

Clustering(61) Variable = APBB1IP MUTATION ANALYSIS
D61V1, survival
                   sevent
clus2                0  1
  APBB1IP MUTATED    1  3
  APBB1IP WILD-TYPE  8 10
  APBB1IP MUTATED APBB1IP WILD-TYPE 
                4                18 
  APBB1IP MUTATED APBB1IP WILD-TYPE 
                3                10 
$`APBB1IP MUTATED`
TCGA-D3-A2J8 TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A29Q 
        8.38         7.00        11.57         8.12 

$`APBB1IP WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A185 
       16.47        28.08         5.39        48.79        39.19         4.27 
TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
        1.08         8.84         9.99         2.43         8.09        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       23.90         9.67         3.52        42.84        16.21        15.39 

  APBB1IP MUTATED APBB1IP WILD-TYPE 
             7.00              1.08 
  APBB1IP MUTATED APBB1IP WILD-TYPE 
            11.57             48.79 
  APBB1IP MUTATED APBB1IP WILD-TYPE 
             8.25             12.69 
[1] "7.0 - 11.6 (8.2)"  "1.1 - 48.8 (12.7)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE"   "APBB1IP MUTATED" "APBB1IP WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE"   "APBB1IP MUTATED"   "APBB1IP MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE"   "APBB1IP MUTATED" "APBB1IP WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE"   "APBB1IP MUTATED" "APBB1IP WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE"   "APBB1IP MUTATED"   "APBB1IP MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE"   "APBB1IP MUTATED" "APBB1IP WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE"   "APBB1IP MUTATED" "APBB1IP WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE"   "APBB1IP MUTATED"   "APBB1IP MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE"   "APBB1IP MUTATED" "APBB1IP WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"APBB1IP WILD-TYPE" "APBB1IP WILD-TYPE" 
[1] "hr=" "2.5"
D61V2, continuous
                   vv
clus                DISTANT METASTASIS
  APBB1IP MUTATED                    0
  APBB1IP WILD-TYPE                  8
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  APBB1IP MUTATED                                                                                          2
  APBB1IP WILD-TYPE                                                                                        7
                   vv
clus                REGIONAL LYMPH NODE
  APBB1IP MUTATED                     3
  APBB1IP WILD-TYPE                  25
D61V3, multiclass
                                                                                          clus
vv                                                                                         APBB1IP MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         APBB1IP WILD-TYPE
  DISTANT METASTASIS                                                                                       8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 7
  REGIONAL LYMPH NODE                                                                                     25
D61V4, binary
                   cls
clus                 0  1
  APBB1IP MUTATED    2  3
  APBB1IP WILD-TYPE 14 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APBB1IP MUTATED      2    3
  APBB1IP WILD-TYPE   14   26
        clus
vv       APBB1IP MUTATED APBB1IP WILD-TYPE
  FEMALE               2                14
  MALE                 3                26
                   vv
clus                N0 N1A N1B N2A N2B N3
  APBB1IP MUTATED    4   0   0   0   1  0
  APBB1IP WILD-TYPE 23   3   4   1   1  5
D61V5, multiclass
D61V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  APBB1IP MUTATED             0       0        1        1        0         0
  APBB1IP WILD-TYPE           1       3        3        5        4         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  APBB1IP MUTATED           2         0         0          0          1
  APBB1IP WILD-TYPE         2         2         1          1          5
                   vv
clus                STAGE IIIC STAGE IV
  APBB1IP MUTATED            0        0
  APBB1IP WILD-TYPE          6        1
D61V7, multiclass

Clustering(62) Variable = ANGPT1 MUTATION ANALYSIS
D62V1, survival
                  sevent
clus2               0  1
  ANGPT1 MUTATED    3  1
  ANGPT1 WILD-TYPE  6 12
  ANGPT1 MUTATED ANGPT1 WILD-TYPE 
               4               18 
  ANGPT1 MUTATED ANGPT1 WILD-TYPE 
               1               12 
$`ANGPT1 MUTATED`
TCGA-EE-A29S TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        9.99        25.28        23.90         9.67 

$`ANGPT1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
        7.00        11.57         4.27         1.08         8.12         8.84 
TCGA-EE-A29V TCGA-EE-A29X TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
        2.43         8.09         3.52        42.84        16.21        15.39 

  ANGPT1 MUTATED ANGPT1 WILD-TYPE 
            9.67             1.08 
  ANGPT1 MUTATED ANGPT1 WILD-TYPE 
           25.28            48.79 
  ANGPT1 MUTATED ANGPT1 WILD-TYPE 
          16.945            8.610 
[1] "9.7 - 25.3 (16.9)" "1.1 - 48.8 (8.6)" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "ANGPT1 MUTATED" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE"   "ANGPT1 MUTATED" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "ANGPT1 MUTATED"   "ANGPT1 MUTATED" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "ANGPT1 MUTATED" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE"   "ANGPT1 MUTATED" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "ANGPT1 MUTATED"   "ANGPT1 MUTATED" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "ANGPT1 MUTATED" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE"   "ANGPT1 MUTATED" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "ANGPT1 MUTATED"   "ANGPT1 MUTATED" "ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"ANGPT1 WILD-TYPE" "ANGPT1 WILD-TYPE" 
[1] "hr=" "3.5"
D62V2, continuous
                  vv
clus               DISTANT METASTASIS
  ANGPT1 MUTATED                    0
  ANGPT1 WILD-TYPE                  8
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ANGPT1 MUTATED                                                                                          1
  ANGPT1 WILD-TYPE                                                                                        8
                  vv
clus               REGIONAL LYMPH NODE
  ANGPT1 MUTATED                     5
  ANGPT1 WILD-TYPE                  23
D62V3, multiclass
                                                                                          clus
vv                                                                                         ANGPT1 MUTATED
  DISTANT METASTASIS                                                                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   5
                                                                                          clus
vv                                                                                         ANGPT1 WILD-TYPE
  DISTANT METASTASIS                                                                                      8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    23
D62V4, binary
                  cls
clus                0  1
  ANGPT1 MUTATED    0  6
  ANGPT1 WILD-TYPE 16 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANGPT1 MUTATED      0    6
  ANGPT1 WILD-TYPE   16   23
        clus
vv       ANGPT1 MUTATED ANGPT1 WILD-TYPE
  FEMALE              0               16
  MALE                6               23
                  vv
clus               N0 N1A N1B N2A N2B N3
  ANGPT1 MUTATED    5   0   1   0   0  0
  ANGPT1 WILD-TYPE 22   3   3   1   2  5
D62V5, multiclass
D62V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ANGPT1 MUTATED             0       0        1        2        1         1
  ANGPT1 WILD-TYPE           1       3        3        4        3         2
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ANGPT1 MUTATED           0         0         0          0          1
  ANGPT1 WILD-TYPE         4         2         1          1          5
                  vv
clus               STAGE IIIC STAGE IV
  ANGPT1 MUTATED            0        0
  ANGPT1 WILD-TYPE          6        1
D62V7, multiclass

Clustering(63) Variable = ARMC4 MUTATION ANALYSIS
D63V1, survival
                 sevent
clus2              0  1
  ARMC4 MUTATED    3  1
  ARMC4 WILD-TYPE  6 12
  ARMC4 MUTATED ARMC4 WILD-TYPE 
              4              18 
  ARMC4 MUTATED ARMC4 WILD-TYPE 
              1              12 
$`ARMC4 MUTATED`
TCGA-DA-A1HV TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A2A2 
       48.79         1.08         8.84        23.90 

$`ARMC4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       11.57         4.27         8.12         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       25.28         9.67         3.52        42.84        16.21        15.39 

  ARMC4 MUTATED ARMC4 WILD-TYPE 
           1.08            2.43 
  ARMC4 MUTATED ARMC4 WILD-TYPE 
          48.79           42.84 
  ARMC4 MUTATED ARMC4 WILD-TYPE 
          16.37            9.83 
[1] "1.1 - 48.8 (16.4)" "2.4 - 42.8 (9.8)" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "ARMC4 MUTATED" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ARMC4 WILD-TYPE"   "ARMC4 MUTATED" "ARMC4 WILD-TYPE"   "ARMC4 MUTATED" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "ARMC4 MUTATED" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "ARMC4 MUTATED" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ARMC4 WILD-TYPE"   "ARMC4 MUTATED" "ARMC4 WILD-TYPE"   "ARMC4 MUTATED" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "ARMC4 MUTATED" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "ARMC4 MUTATED" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ARMC4 WILD-TYPE"   "ARMC4 MUTATED" "ARMC4 WILD-TYPE"   "ARMC4 MUTATED" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "ARMC4 MUTATED" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ARMC4 WILD-TYPE" "ARMC4 WILD-TYPE" 
[1] "hr=" "3"  
D63V2, continuous
                 vv
clus              DISTANT METASTASIS
  ARMC4 MUTATED                    3
  ARMC4 WILD-TYPE                  5
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ARMC4 MUTATED                                                                                          1
  ARMC4 WILD-TYPE                                                                                        8
                 vv
clus              REGIONAL LYMPH NODE
  ARMC4 MUTATED                     7
  ARMC4 WILD-TYPE                  21
D63V3, multiclass
                                                                                          clus
vv                                                                                         ARMC4 MUTATED
  DISTANT METASTASIS                                                                                   3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  7
                                                                                          clus
vv                                                                                         ARMC4 WILD-TYPE
  DISTANT METASTASIS                                                                                     5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               8
  REGIONAL LYMPH NODE                                                                                   21
D63V4, binary
                 cls
clus               0  1
  ARMC4 MUTATED    4  7
  ARMC4 WILD-TYPE 12 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC4 MUTATED      4    7
  ARMC4 WILD-TYPE   12   22
        clus
vv       ARMC4 MUTATED ARMC4 WILD-TYPE
  FEMALE             4              12
  MALE               7              22
                 vv
clus              N0 N1A N1B N2A N2B N3
  ARMC4 MUTATED    5   0   3   0   1  1
  ARMC4 WILD-TYPE 22   3   1   1   1  4
D63V5, multiclass
D63V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ARMC4 MUTATED             0       1        1        0        1         0
  ARMC4 WILD-TYPE           1       2        3        6        3         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ARMC4 MUTATED           1         1         1          0          2
  ARMC4 WILD-TYPE         3         1         0          1          4
                 vv
clus              STAGE IIIC STAGE IV
  ARMC4 MUTATED            2        0
  ARMC4 WILD-TYPE          4        1
D63V7, multiclass

Clustering(64) Variable = CYP4X1 MUTATION ANALYSIS
D64V1, survival
                  sevent
clus2               0  1
  CYP4X1 MUTATED    1  1
  CYP4X1 WILD-TYPE  8 12
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               2               20 
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               1               12 
$`CYP4X1 MUTATED`
TCGA-D3-A2J8 TCGA-D3-A3MV 
        8.38         5.39 

$`CYP4X1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       16.47        28.08        48.79        39.19         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        4.27         1.08         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
            5.39             1.08 
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
            8.38            48.79 
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
           6.885           10.780 
[1] "5.4 - 8.4 (6.9)"   "1.1 - 48.8 (10.8)"
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE"   "CYP4X1 MUTATED"   "CYP4X1 MUTATED" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE"   "CYP4X1 MUTATED"   "CYP4X1 MUTATED" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE"   "CYP4X1 MUTATED"   "CYP4X1 MUTATED" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
[1] "Remove cluster labels:" "CYP4X1 MUTATED"        
clus
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               2               20 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-DA-A1HV       TCGA-DA-A1I1 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-DA-A3F3       TCGA-EE-A17X       TCGA-EE-A185       TCGA-EE-A29L 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-EE-A29Q       TCGA-EE-A29R       TCGA-EE-A29S       TCGA-EE-A29V 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-EE-A29X       TCGA-EE-A2A1       TCGA-EE-A2A2       TCGA-EE-A2A5 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
      TCGA-ER-A19D       TCGA-ER-A19N       TCGA-GN-A267       TCGA-GN-A268 
"CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" "CYP4X1 WILD-TYPE" 
D64V2, continuous
                  vv
clus               DISTANT METASTASIS
  CYP4X1 MUTATED                    0
  CYP4X1 WILD-TYPE                  8
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CYP4X1 MUTATED                                                                                          2
  CYP4X1 WILD-TYPE                                                                                        7
                  vv
clus               REGIONAL LYMPH NODE
  CYP4X1 MUTATED                     2
  CYP4X1 WILD-TYPE                  26
D64V3, multiclass
                                                                                          clus
vv                                                                                         CYP4X1 MUTATED
  DISTANT METASTASIS                                                                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              2
  REGIONAL LYMPH NODE                                                                                   2
                                                                                          clus
vv                                                                                         CYP4X1 WILD-TYPE
  DISTANT METASTASIS                                                                                      8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                7
  REGIONAL LYMPH NODE                                                                                    26
D64V4, binary
                  cls
clus                0  1
  CYP4X1 MUTATED    3  1
  CYP4X1 WILD-TYPE 13 28
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4X1 MUTATED      3    1
  CYP4X1 WILD-TYPE   13   28
        clus
vv       CYP4X1 MUTATED CYP4X1 WILD-TYPE
  FEMALE              3               13
  MALE                1               28
                  vv
clus               N0 N1A N1B N2A N2B N3
  CYP4X1 MUTATED    3   0   0   1   0  0
  CYP4X1 WILD-TYPE 24   3   4   0   2  5
D64V5, multiclass
D64V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CYP4X1 MUTATED             0       0        0        1        0         1
  CYP4X1 WILD-TYPE           1       3        4        5        4         2
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CYP4X1 MUTATED           1         0         0          0          1
  CYP4X1 WILD-TYPE         3         2         1          1          5
                  vv
clus               STAGE IIIC STAGE IV
  CYP4X1 MUTATED            0        0
  CYP4X1 WILD-TYPE          6        1
D64V7, multiclass

Clustering(65) Variable = DSG1 MUTATION ANALYSIS
D65V1, survival
                sevent
clus2             0  1
  DSG1 MUTATED    2  2
  DSG1 WILD-TYPE  7 11
  DSG1 MUTATED DSG1 WILD-TYPE 
             4             18 
  DSG1 MUTATED DSG1 WILD-TYPE 
             2             11 
$`DSG1 MUTATED`
TCGA-D3-A3MV TCGA-DA-A1HV TCGA-EE-A185 TCGA-EE-A2A5 
        5.39        48.79         4.27         9.67 

$`DSG1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       16.47        28.08         8.38        39.19         7.00        11.57 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
        1.08         8.12         8.84         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       25.28        23.90         3.52        42.84        16.21        15.39 

  DSG1 MUTATED DSG1 WILD-TYPE 
          4.27           1.08 
  DSG1 MUTATED DSG1 WILD-TYPE 
         48.79          42.84 
  DSG1 MUTATED DSG1 WILD-TYPE 
          7.53          10.78 
[1] "4.3 - 48.8 (7.5)"  "1.1 - 42.8 (10.8)"
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"DSG1 WILD-TYPE" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE"   "DSG1 MUTATED" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "DSG1 MUTATED" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
  "DSG1 MUTATED" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"DSG1 WILD-TYPE" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"DSG1 WILD-TYPE"   "DSG1 MUTATED" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"DSG1 WILD-TYPE" "DSG1 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"DSG1 WILD-TYPE" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE"   "DSG1 MUTATED" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "DSG1 MUTATED" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
  "DSG1 MUTATED" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"DSG1 WILD-TYPE" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"DSG1 WILD-TYPE"   "DSG1 MUTATED" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"DSG1 WILD-TYPE" "DSG1 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"DSG1 WILD-TYPE" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE"   "DSG1 MUTATED" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "DSG1 MUTATED" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
  "DSG1 MUTATED" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"DSG1 WILD-TYPE" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"DSG1 WILD-TYPE"   "DSG1 MUTATED" "DSG1 WILD-TYPE" "DSG1 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"DSG1 WILD-TYPE" "DSG1 WILD-TYPE" 
[1] "hr=" "1"  
D65V2, continuous
                vv
clus             DISTANT METASTASIS
  DSG1 MUTATED                    0
  DSG1 WILD-TYPE                  8
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DSG1 MUTATED                                                                                          2
  DSG1 WILD-TYPE                                                                                        7
                vv
clus             REGIONAL LYMPH NODE
  DSG1 MUTATED                     4
  DSG1 WILD-TYPE                  24
D65V3, multiclass
                                                                                          clus
vv                                                                                         DSG1 MUTATED
  DISTANT METASTASIS                                                                                  0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            2
  REGIONAL LYMPH NODE                                                                                 4
                                                                                          clus
vv                                                                                         DSG1 WILD-TYPE
  DISTANT METASTASIS                                                                                    8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              7
  REGIONAL LYMPH NODE                                                                                  24
D65V4, binary
                cls
clus              0  1
  DSG1 MUTATED    3  3
  DSG1 WILD-TYPE 13 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG1 MUTATED      3    3
  DSG1 WILD-TYPE   13   26
        clus
vv       DSG1 MUTATED DSG1 WILD-TYPE
  FEMALE            3             13
  MALE              3             26
                vv
clus             N0 N1A N1B N2A N2B N3
  DSG1 MUTATED    2   1   0   1   1  1
  DSG1 WILD-TYPE 25   2   4   0   1  4
D65V5, multiclass
D65V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DSG1 MUTATED             0       0        0        1        1         0
  DSG1 WILD-TYPE           1       3        4        5        3         3
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DSG1 MUTATED           0         0         0          0          3          1
  DSG1 WILD-TYPE         4         2         1          1          3          5
                vv
clus             STAGE IV
  DSG1 MUTATED          0
  DSG1 WILD-TYPE        1
D65V7, multiclass

Clustering(66) Variable = ADAM7 MUTATION ANALYSIS
D66V1, survival
                 sevent
clus2              0  1
  ADAM7 MUTATED    3  2
  ADAM7 WILD-TYPE  6 11
  ADAM7 MUTATED ADAM7 WILD-TYPE 
              5              17 
  ADAM7 MUTATED ADAM7 WILD-TYPE 
              2              11 
$`ADAM7 MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1I1 TCGA-EE-A29S TCGA-EE-A2A1 
       28.08         8.38        39.19         9.99        25.28 

$`ADAM7 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 
       16.47         5.39        48.79         7.00        11.57         4.27 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 
        1.08         8.12         8.84         2.43         8.09        23.90 
TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
        9.67         3.52        42.84        16.21        15.39 

  ADAM7 MUTATED ADAM7 WILD-TYPE 
           8.38            1.08 
  ADAM7 MUTATED ADAM7 WILD-TYPE 
          39.19           48.79 
  ADAM7 MUTATED ADAM7 WILD-TYPE 
          25.28            8.84 
[1] "8.4 - 39.2 (25.3)" "1.1 - 48.8 (8.8)" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ADAM7 WILD-TYPE"   "ADAM7 MUTATED"   "ADAM7 MUTATED" "ADAM7 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"ADAM7 WILD-TYPE"   "ADAM7 MUTATED" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "ADAM7 MUTATED" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE"   "ADAM7 MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ADAM7 WILD-TYPE"   "ADAM7 MUTATED"   "ADAM7 MUTATED" "ADAM7 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"ADAM7 WILD-TYPE"   "ADAM7 MUTATED" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "ADAM7 MUTATED" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE"   "ADAM7 MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"ADAM7 WILD-TYPE"   "ADAM7 MUTATED"   "ADAM7 MUTATED" "ADAM7 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"ADAM7 WILD-TYPE"   "ADAM7 MUTATED" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "ADAM7 MUTATED" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE"   "ADAM7 MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"ADAM7 WILD-TYPE" "ADAM7 WILD-TYPE" 
[1] "hr=" "2.7"
D66V2, continuous
                 vv
clus              DISTANT METASTASIS
  ADAM7 MUTATED                    0
  ADAM7 WILD-TYPE                  8
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ADAM7 MUTATED                                                                                          2
  ADAM7 WILD-TYPE                                                                                        7
                 vv
clus              REGIONAL LYMPH NODE
  ADAM7 MUTATED                     8
  ADAM7 WILD-TYPE                  20
D66V3, multiclass
                                                                                          clus
vv                                                                                         ADAM7 MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  8
                                                                                          clus
vv                                                                                         ADAM7 WILD-TYPE
  DISTANT METASTASIS                                                                                     8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   20
D66V4, binary
                 cls
clus               0  1
  ADAM7 MUTATED    1  9
  ADAM7 WILD-TYPE 15 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADAM7 MUTATED      1    9
  ADAM7 WILD-TYPE   15   20
        clus
vv       ADAM7 MUTATED ADAM7 WILD-TYPE
  FEMALE             1              15
  MALE               9              20
                 vv
clus              N0 N1A N1B N2A N2B N3
  ADAM7 MUTATED    7   1   0   0   0  2
  ADAM7 WILD-TYPE 20   2   4   1   2  3
D66V5, multiclass
D66V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ADAM7 MUTATED             0       0        1        2        2         1
  ADAM7 WILD-TYPE           1       3        3        4        2         2
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ADAM7 MUTATED           0         1         0          0          1
  ADAM7 WILD-TYPE         4         1         1          1          5
                 vv
clus              STAGE IIIC STAGE IV
  ADAM7 MUTATED            1        1
  ADAM7 WILD-TYPE          5        0
D66V7, multiclass

Clustering(67) Variable = KCNQ5 MUTATION ANALYSIS
D67V1, survival
                 sevent
clus2              0  1
  KCNQ5 MUTATED    3  0
  KCNQ5 WILD-TYPE  6 13
  KCNQ5 MUTATED KCNQ5 WILD-TYPE 
              3              19 
  KCNQ5 MUTATED KCNQ5 WILD-TYPE 
              0              13 
$`KCNQ5 MUTATED`
TCGA-DA-A1I1 TCGA-EE-A29S TCGA-EE-A2A2 
       39.19         9.99        23.90 

$`KCNQ5 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        48.79         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       11.57         4.27         1.08         8.12         8.84         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
        8.09        25.28         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  KCNQ5 MUTATED KCNQ5 WILD-TYPE 
           9.99            1.08 
  KCNQ5 MUTATED KCNQ5 WILD-TYPE 
          39.19           48.79 
  KCNQ5 MUTATED KCNQ5 WILD-TYPE 
          23.90            8.84 
[1] "10.0 - 39.2 (23.9)" "1.1 - 48.8 (8.8)"  
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"KCNQ5 WILD-TYPE"   "KCNQ5 MUTATED" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "KCNQ5 MUTATED" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "KCNQ5 MUTATED" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"KCNQ5 WILD-TYPE"   "KCNQ5 MUTATED" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "KCNQ5 MUTATED" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "KCNQ5 MUTATED" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"KCNQ5 WILD-TYPE"   "KCNQ5 MUTATED" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "KCNQ5 MUTATED" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "KCNQ5 MUTATED" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"KCNQ5 WILD-TYPE" "KCNQ5 WILD-TYPE" 
[1] "hr="     "2.6e+08"
D67V2, continuous
                 vv
clus              DISTANT METASTASIS
  KCNQ5 MUTATED                    0
  KCNQ5 WILD-TYPE                  8
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  KCNQ5 MUTATED                                                                                          2
  KCNQ5 WILD-TYPE                                                                                        7
                 vv
clus              REGIONAL LYMPH NODE
  KCNQ5 MUTATED                     6
  KCNQ5 WILD-TYPE                  22
D67V3, multiclass
                                                                                          clus
vv                                                                                         KCNQ5 MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  6
                                                                                          clus
vv                                                                                         KCNQ5 WILD-TYPE
  DISTANT METASTASIS                                                                                     8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   22
D67V4, binary
                 cls
clus               0  1
  KCNQ5 MUTATED    3  5
  KCNQ5 WILD-TYPE 13 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNQ5 MUTATED      3    5
  KCNQ5 WILD-TYPE   13   24
        clus
vv       KCNQ5 MUTATED KCNQ5 WILD-TYPE
  FEMALE             3              13
  MALE               5              24
                 vv
clus              N0 N1A N1B N2A N2B N3
  KCNQ5 MUTATED    5   1   1   0   0  1
  KCNQ5 WILD-TYPE 22   2   3   1   2  4
D67V5, multiclass
D67V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  KCNQ5 MUTATED             0       1        1        0        1         1
  KCNQ5 WILD-TYPE           1       2        3        6        3         2
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  KCNQ5 MUTATED           1         0         0          0          2
  KCNQ5 WILD-TYPE         3         2         1          1          4
                 vv
clus              STAGE IIIC STAGE IV
  KCNQ5 MUTATED            1        0
  KCNQ5 WILD-TYPE          5        1
D67V7, multiclass

Clustering(68) Variable = POF1B MUTATION ANALYSIS
D68V1, survival
                 sevent
clus2              0  1
  POF1B MUTATED    2  1
  POF1B WILD-TYPE  7 12
  POF1B MUTATED POF1B WILD-TYPE 
              3              19 
  POF1B MUTATED POF1B WILD-TYPE 
              1              12 
$`POF1B MUTATED`
TCGA-D3-A3MV TCGA-EE-A29S TCGA-ER-A19D 
        5.39         9.99         3.52 

$`POF1B WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       11.57         4.27         1.08         8.12         8.84         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19N TCGA-GN-A267 
        8.09        25.28        23.90         9.67        42.84        16.21 
TCGA-GN-A268 
       15.39 

  POF1B MUTATED POF1B WILD-TYPE 
           3.52            1.08 
  POF1B MUTATED POF1B WILD-TYPE 
           9.99           48.79 
  POF1B MUTATED POF1B WILD-TYPE 
           5.39           11.57 
[1] "3.5 - 10.0 (5.4)"  "1.1 - 48.8 (11.6)"
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE"   "POF1B MUTATED" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "POF1B MUTATED" "POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"POF1B WILD-TYPE" "POF1B WILD-TYPE"   "POF1B MUTATED" "POF1B WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"POF1B WILD-TYPE" "POF1B WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE"   "POF1B MUTATED" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "POF1B MUTATED" "POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"POF1B WILD-TYPE" "POF1B WILD-TYPE"   "POF1B MUTATED" "POF1B WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"POF1B WILD-TYPE" "POF1B WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE"   "POF1B MUTATED" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "POF1B MUTATED" "POF1B WILD-TYPE" "POF1B WILD-TYPE" "POF1B WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"POF1B WILD-TYPE" "POF1B WILD-TYPE"   "POF1B MUTATED" "POF1B WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"POF1B WILD-TYPE" "POF1B WILD-TYPE" 
[1] "hr=" "1.3"
D68V2, continuous
                 vv
clus              DISTANT METASTASIS
  POF1B MUTATED                    0
  POF1B WILD-TYPE                  8
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  POF1B MUTATED                                                                                          3
  POF1B WILD-TYPE                                                                                        6
                 vv
clus              REGIONAL LYMPH NODE
  POF1B MUTATED                     5
  POF1B WILD-TYPE                  23
D68V3, multiclass
                                                                                          clus
vv                                                                                         POF1B MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             3
  REGIONAL LYMPH NODE                                                                                  5
                                                                                          clus
vv                                                                                         POF1B WILD-TYPE
  DISTANT METASTASIS                                                                                     8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               6
  REGIONAL LYMPH NODE                                                                                   23
D68V4, binary
                 cls
clus               0  1
  POF1B MUTATED    4  4
  POF1B WILD-TYPE 12 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POF1B MUTATED      4    4
  POF1B WILD-TYPE   12   25
        clus
vv       POF1B MUTATED POF1B WILD-TYPE
  FEMALE             4              12
  MALE               4              25
                 vv
clus              N0 N1A N1B N2A N2B N3
  POF1B MUTATED    5   1   0   1   0  0
  POF1B WILD-TYPE 22   2   4   0   2  5
D68V5, multiclass
D68V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  POF1B MUTATED             0       0        2        1        0         1
  POF1B WILD-TYPE           1       3        2        5        4         2
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  POF1B MUTATED           1         0         0          0          2
  POF1B WILD-TYPE         3         2         1          1          4
                 vv
clus              STAGE IIIC STAGE IV
  POF1B MUTATED            0        0
  POF1B WILD-TYPE          6        1
D68V7, multiclass

Clustering(69) Variable = TCEB3C MUTATION ANALYSIS
D69V1, survival
                  sevent
clus2               0  1
  TCEB3C MUTATED    3  1
  TCEB3C WILD-TYPE  6 12
  TCEB3C MUTATED TCEB3C WILD-TYPE 
               4               18 
  TCEB3C MUTATED TCEB3C WILD-TYPE 
               1               12 
$`TCEB3C MUTATED`
TCGA-D3-A3MV TCGA-EE-A29L TCGA-EE-A29S TCGA-EE-A2A2 
        5.39         1.08         9.99        23.90 

$`TCEB3C WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29X 
       11.57         4.27         8.12         8.84         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       25.28         9.67         3.52        42.84        16.21        15.39 

  TCEB3C MUTATED TCEB3C WILD-TYPE 
            1.08             2.43 
  TCEB3C MUTATED TCEB3C WILD-TYPE 
           23.90            48.79 
  TCEB3C MUTATED TCEB3C WILD-TYPE 
            7.69            10.62 
[1] "1.1 - 23.9 (7.7)"  "2.4 - 48.8 (10.6)"
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE"   "TCEB3C MUTATED" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"TCEB3C WILD-TYPE"   "TCEB3C MUTATED" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "TCEB3C MUTATED" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "TCEB3C MUTATED" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE"   "TCEB3C MUTATED" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"TCEB3C WILD-TYPE"   "TCEB3C MUTATED" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "TCEB3C MUTATED" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "TCEB3C MUTATED" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE"   "TCEB3C MUTATED" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"TCEB3C WILD-TYPE"   "TCEB3C MUTATED" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "TCEB3C MUTATED" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "TCEB3C MUTATED" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"TCEB3C WILD-TYPE" "TCEB3C WILD-TYPE" 
[1] "hr=" "1.8"
D69V2, continuous
                  vv
clus               DISTANT METASTASIS
  TCEB3C MUTATED                    1
  TCEB3C WILD-TYPE                  7
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  TCEB3C MUTATED                                                                                          1
  TCEB3C WILD-TYPE                                                                                        8
                  vv
clus               REGIONAL LYMPH NODE
  TCEB3C MUTATED                     4
  TCEB3C WILD-TYPE                  24
D69V3, multiclass
                                                                                          clus
vv                                                                                         TCEB3C MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   4
                                                                                          clus
vv                                                                                         TCEB3C WILD-TYPE
  DISTANT METASTASIS                                                                                      7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    24
D69V4, binary
                  cls
clus                0  1
  TCEB3C MUTATED    1  5
  TCEB3C WILD-TYPE 15 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEB3C MUTATED      1    5
  TCEB3C WILD-TYPE   15   24
        clus
vv       TCEB3C MUTATED TCEB3C WILD-TYPE
  FEMALE              1               15
  MALE                5               24
                  vv
clus               N0 N1A N1B N2A N2B N3
  TCEB3C MUTATED    3   0   1   1   0  1
  TCEB3C WILD-TYPE 24   3   3   0   2  4
D69V5, multiclass
D69V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  TCEB3C MUTATED             0       0        0        0        1         1
  TCEB3C WILD-TYPE           1       3        4        6        3         2
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  TCEB3C MUTATED           0         1         0          0          2
  TCEB3C WILD-TYPE         4         1         1          1          4
                  vv
clus               STAGE IIIC STAGE IV
  TCEB3C MUTATED            1        0
  TCEB3C WILD-TYPE          5        1
D69V7, multiclass

Clustering(70) Variable = F2RL1 MUTATION ANALYSIS
D70V1, survival
                 sevent
clus2              0  1
  F2RL1 MUTATED    0  1
  F2RL1 WILD-TYPE  9 12
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              1              21 
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              1              12 
$`F2RL1 MUTATED`
TCGA-D3-A1Q1 
       16.47 

$`F2RL1 WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       28.08         8.38         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        2.43         8.09        25.28        23.90         9.67         3.52 
TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       42.84        16.21        15.39 

  F2RL1 MUTATED F2RL1 WILD-TYPE 
          16.47            1.08 
  F2RL1 MUTATED F2RL1 WILD-TYPE 
          16.47           48.79 
  F2RL1 MUTATED F2RL1 WILD-TYPE 
          16.47            9.67 
[1] "16.5 - 16.5 (16.5)" "1.1 - 48.8 (9.7)"  
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
  "F2RL1 MUTATED" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
  "F2RL1 MUTATED" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
  "F2RL1 MUTATED" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
[1] "Remove cluster labels:" "F2RL1 MUTATED"         
clus
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              1              21 
     TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV      TCGA-DA-A1HV 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X      TCGA-EE-A185 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R      TCGA-EE-A29S 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1      TCGA-EE-A2A2 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N      TCGA-GN-A267 
"F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" "F2RL1 WILD-TYPE" 
     TCGA-GN-A268 
"F2RL1 WILD-TYPE" 
D70V2, continuous
                 vv
clus              DISTANT METASTASIS
  F2RL1 MUTATED                    0
  F2RL1 WILD-TYPE                  8
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  F2RL1 MUTATED                                                                                          2
  F2RL1 WILD-TYPE                                                                                        7
                 vv
clus              REGIONAL LYMPH NODE
  F2RL1 MUTATED                     3
  F2RL1 WILD-TYPE                  25
D70V3, multiclass
                                                                                          clus
vv                                                                                         F2RL1 MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         F2RL1 WILD-TYPE
  DISTANT METASTASIS                                                                                     8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   25
D70V4, binary
                 cls
clus               0  1
  F2RL1 MUTATED    3  2
  F2RL1 WILD-TYPE 13 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  F2RL1 MUTATED      3    2
  F2RL1 WILD-TYPE   13   27
        clus
vv       F2RL1 MUTATED F2RL1 WILD-TYPE
  FEMALE             3              13
  MALE               2              27
                 vv
clus              N0 N1A N1B N2A N2B N3
  F2RL1 MUTATED    3   0   0   0   0  1
  F2RL1 WILD-TYPE 24   3   4   1   2  4
D70V5, multiclass
D70V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  F2RL1 MUTATED             0       1        0        0        0         0
  F2RL1 WILD-TYPE           1       2        4        6        4         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  F2RL1 MUTATED           1         1         0          0          0
  F2RL1 WILD-TYPE         3         1         1          1          6
                 vv
clus              STAGE IIIC STAGE IV
  F2RL1 MUTATED            1        0
  F2RL1 WILD-TYPE          5        1
D70V7, multiclass

Clustering(71) Variable = SNCAIP MUTATION ANALYSIS
D71V1, survival
                  sevent
clus2               0  1
  SNCAIP MUTATED    2  2
  SNCAIP WILD-TYPE  7 11
  SNCAIP MUTATED SNCAIP WILD-TYPE 
               4               18 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
               2               11 
$`SNCAIP MUTATED`
TCGA-D3-A1Q8 TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A2A1 
       28.08        39.19         7.00        25.28 

$`SNCAIP WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A185 
       16.47         8.38         5.39        48.79        11.57         4.27 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
        1.08         8.12         8.84         9.99         2.43         8.09 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       23.90         9.67         3.52        42.84        16.21        15.39 

  SNCAIP MUTATED SNCAIP WILD-TYPE 
            7.00             1.08 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
           39.19            48.79 
  SNCAIP MUTATED SNCAIP WILD-TYPE 
          26.680            9.255 
[1] "7.0 - 39.2 (26.7)" "1.1 - 48.8 (9.3)" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"SNCAIP WILD-TYPE"   "SNCAIP MUTATED" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"SNCAIP WILD-TYPE"   "SNCAIP MUTATED"   "SNCAIP MUTATED" "SNCAIP WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE"   "SNCAIP MUTATED" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"SNCAIP WILD-TYPE"   "SNCAIP MUTATED" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"SNCAIP WILD-TYPE"   "SNCAIP MUTATED"   "SNCAIP MUTATED" "SNCAIP WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE"   "SNCAIP MUTATED" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"SNCAIP WILD-TYPE"   "SNCAIP MUTATED" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"SNCAIP WILD-TYPE"   "SNCAIP MUTATED"   "SNCAIP MUTATED" "SNCAIP WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE"   "SNCAIP MUTATED" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"SNCAIP WILD-TYPE" "SNCAIP WILD-TYPE" 
[1] "hr=" "2.2"
D71V2, continuous
                  vv
clus               DISTANT METASTASIS
  SNCAIP MUTATED                    1
  SNCAIP WILD-TYPE                  7
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  SNCAIP MUTATED                                                                                          2
  SNCAIP WILD-TYPE                                                                                        7
                  vv
clus               REGIONAL LYMPH NODE
  SNCAIP MUTATED                     6
  SNCAIP WILD-TYPE                  22
D71V3, multiclass
                                                                                          clus
vv                                                                                         SNCAIP MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              2
  REGIONAL LYMPH NODE                                                                                   6
                                                                                          clus
vv                                                                                         SNCAIP WILD-TYPE
  DISTANT METASTASIS                                                                                      7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                7
  REGIONAL LYMPH NODE                                                                                    22
D71V4, binary
                  cls
clus                0  1
  SNCAIP MUTATED    1  8
  SNCAIP WILD-TYPE 15 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNCAIP MUTATED      1    8
  SNCAIP WILD-TYPE   15   21
        clus
vv       SNCAIP MUTATED SNCAIP WILD-TYPE
  FEMALE              1               15
  MALE                8               21
                  vv
clus               N0 N1A N1B N2A N2B N3
  SNCAIP MUTATED    4   1   0   0   1  2
  SNCAIP WILD-TYPE 23   2   4   1   1  3
D71V5, multiclass
D71V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  SNCAIP MUTATED             0       0        1        1        1         1
  SNCAIP WILD-TYPE           1       3        3        5        3         2
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  SNCAIP MUTATED           0         0         0          0          2
  SNCAIP WILD-TYPE         4         2         1          1          4
                  vv
clus               STAGE IIIC STAGE IV
  SNCAIP MUTATED            1        1
  SNCAIP WILD-TYPE          5        0
D71V7, multiclass

Clustering(72) Variable = LOC649330 MUTATION ANALYSIS
D72V1, survival
                     sevent
clus2                  0  1
  LOC649330 MUTATED    2  3
  LOC649330 WILD-TYPE  7 10
  LOC649330 MUTATED LOC649330 WILD-TYPE 
                  5                  17 
  LOC649330 MUTATED LOC649330 WILD-TYPE 
                  3                  10 
$`LOC649330 MUTATED`
TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-EE-A29V TCGA-EE-A2A1 TCGA-GN-A268 
        8.38        48.79         2.43        25.28        15.39 

$`LOC649330 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       16.47        28.08         5.39        39.19         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X 
        4.27         1.08         8.12         8.84         9.99         8.09 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
       23.90         9.67         3.52        42.84        16.21 

  LOC649330 MUTATED LOC649330 WILD-TYPE 
               2.43                1.08 
  LOC649330 MUTATED LOC649330 WILD-TYPE 
              48.79               42.84 
  LOC649330 MUTATED LOC649330 WILD-TYPE 
              15.39                9.67 
[1] "2.4 - 48.8 (15.4)" "1.1 - 42.8 (9.7)" 
         TCGA-D3-A1Q1          TCGA-D3-A1Q8          TCGA-D3-A2J8 
"LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE"   "LOC649330 MUTATED" 
         TCGA-D3-A3MV          TCGA-DA-A1HV          TCGA-DA-A1I1 
"LOC649330 WILD-TYPE"   "LOC649330 MUTATED" "LOC649330 WILD-TYPE" 
         TCGA-DA-A3F3          TCGA-EE-A17X          TCGA-EE-A185 
"LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" 
         TCGA-EE-A29L          TCGA-EE-A29Q          TCGA-EE-A29R 
"LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" 
         TCGA-EE-A29S          TCGA-EE-A29V          TCGA-EE-A29X 
"LOC649330 WILD-TYPE"   "LOC649330 MUTATED" "LOC649330 WILD-TYPE" 
         TCGA-EE-A2A1          TCGA-EE-A2A2          TCGA-EE-A2A5 
  "LOC649330 MUTATED" "LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" 
         TCGA-ER-A19D          TCGA-ER-A19N          TCGA-GN-A267 
"LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" 
         TCGA-GN-A268 
  "LOC649330 MUTATED" 
         TCGA-D3-A1Q1          TCGA-D3-A1Q8          TCGA-D3-A2J8 
"LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE"   "LOC649330 MUTATED" 
         TCGA-D3-A3MV          TCGA-DA-A1HV          TCGA-DA-A1I1 
"LOC649330 WILD-TYPE"   "LOC649330 MUTATED" "LOC649330 WILD-TYPE" 
         TCGA-DA-A3F3          TCGA-EE-A17X          TCGA-EE-A185 
"LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" 
         TCGA-EE-A29L          TCGA-EE-A29Q          TCGA-EE-A29R 
"LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" 
         TCGA-EE-A29S          TCGA-EE-A29V          TCGA-EE-A29X 
"LOC649330 WILD-TYPE"   "LOC649330 MUTATED" "LOC649330 WILD-TYPE" 
         TCGA-EE-A2A1          TCGA-EE-A2A2          TCGA-EE-A2A5 
  "LOC649330 MUTATED" "LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" 
         TCGA-ER-A19D          TCGA-ER-A19N          TCGA-GN-A267 
"LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" 
         TCGA-GN-A268 
  "LOC649330 MUTATED" 
         TCGA-D3-A1Q1          TCGA-D3-A1Q8          TCGA-D3-A2J8 
"LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE"   "LOC649330 MUTATED" 
         TCGA-D3-A3MV          TCGA-DA-A1HV          TCGA-DA-A1I1 
"LOC649330 WILD-TYPE"   "LOC649330 MUTATED" "LOC649330 WILD-TYPE" 
         TCGA-DA-A3F3          TCGA-EE-A17X          TCGA-EE-A185 
"LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" 
         TCGA-EE-A29L          TCGA-EE-A29Q          TCGA-EE-A29R 
"LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" 
         TCGA-EE-A29S          TCGA-EE-A29V          TCGA-EE-A29X 
"LOC649330 WILD-TYPE"   "LOC649330 MUTATED" "LOC649330 WILD-TYPE" 
         TCGA-EE-A2A1          TCGA-EE-A2A2          TCGA-EE-A2A5 
  "LOC649330 MUTATED" "LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" 
         TCGA-ER-A19D          TCGA-ER-A19N          TCGA-GN-A267 
"LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" "LOC649330 WILD-TYPE" 
         TCGA-GN-A268 
  "LOC649330 MUTATED" 
[1] "hr=" "1.1"
D72V2, continuous
                     vv
clus                  DISTANT METASTASIS
  LOC649330 MUTATED                    1
  LOC649330 WILD-TYPE                  7
                     vv
clus                  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  LOC649330 MUTATED                                                                                          1
  LOC649330 WILD-TYPE                                                                                        8
                     vv
clus                  REGIONAL LYMPH NODE
  LOC649330 MUTATED                     5
  LOC649330 WILD-TYPE                  23
D72V3, multiclass
                                                                                          clus
vv                                                                                         LOC649330 MUTATED
  DISTANT METASTASIS                                                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 1
  REGIONAL LYMPH NODE                                                                                      5
                                                                                          clus
vv                                                                                         LOC649330 WILD-TYPE
  DISTANT METASTASIS                                                                                         7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                   8
  REGIONAL LYMPH NODE                                                                                       23
D72V4, binary
                     cls
clus                   0  1
  LOC649330 MUTATED    2  5
  LOC649330 WILD-TYPE 14 24
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  LOC649330 MUTATED      2    5
  LOC649330 WILD-TYPE   14   24
        clus
vv       LOC649330 MUTATED LOC649330 WILD-TYPE
  FEMALE                 2                  14
  MALE                   5                  24
                     vv
clus                  N0 N1A N1B N2A N2B N3
  LOC649330 MUTATED    3   1   1   0   1  0
  LOC649330 WILD-TYPE 24   2   3   1   1  5
D72V5, multiclass
D72V6, continuous
                     vv
clus                  I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  LOC649330 MUTATED             0       0        0        2        0         0
  LOC649330 WILD-TYPE           1       3        4        4        4         3
                     vv
clus                  STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  LOC649330 MUTATED           1         0         0          0          2
  LOC649330 WILD-TYPE         3         2         1          1          4
                     vv
clus                  STAGE IIIC STAGE IV
  LOC649330 MUTATED            1        0
  LOC649330 WILD-TYPE          5        1
D72V7, multiclass

Clustering(73) Variable = UGT2A3 MUTATION ANALYSIS
D73V1, survival
                  sevent
clus2               0  1
  UGT2A3 MUTATED    1  0
  UGT2A3 WILD-TYPE  8 13
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
               1               21 
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
               0               13 
$`UGT2A3 MUTATED`
TCGA-EE-A2A2 
        23.9 

$`UGT2A3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
        7.00        11.57         4.27         1.08         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D 
        9.99         2.43         8.09        25.28         9.67         3.52 
TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       42.84        16.21        15.39 

  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
           23.90             1.08 
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
           23.90            48.79 
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
           23.90             9.67 
[1] "23.9 - 23.9 (23.9)" "1.1 - 48.8 (9.7)"  
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "UGT2A3 MUTATED" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "UGT2A3 MUTATED" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
  "UGT2A3 MUTATED" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
[1] "Remove cluster labels:" "UGT2A3 MUTATED"        
clus
  UGT2A3 MUTATED UGT2A3 WILD-TYPE 
               1               21 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N       TCGA-GN-A267 
"UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" "UGT2A3 WILD-TYPE" 
      TCGA-GN-A268 
"UGT2A3 WILD-TYPE" 
D73V2, continuous
                  vv
clus               DISTANT METASTASIS
  UGT2A3 MUTATED                    1
  UGT2A3 WILD-TYPE                  7
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  UGT2A3 MUTATED                                                                                          0
  UGT2A3 WILD-TYPE                                                                                        9
                  vv
clus               REGIONAL LYMPH NODE
  UGT2A3 MUTATED                     5
  UGT2A3 WILD-TYPE                  23
D73V3, multiclass
                                                                                          clus
vv                                                                                         UGT2A3 MUTATED
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              0
  REGIONAL LYMPH NODE                                                                                   5
                                                                                          clus
vv                                                                                         UGT2A3 WILD-TYPE
  DISTANT METASTASIS                                                                                      7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                9
  REGIONAL LYMPH NODE                                                                                    23
D73V4, binary
                  cls
clus                0  1
  UGT2A3 MUTATED    1  5
  UGT2A3 WILD-TYPE 15 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A3 MUTATED      1    5
  UGT2A3 WILD-TYPE   15   24
        clus
vv       UGT2A3 MUTATED UGT2A3 WILD-TYPE
  FEMALE              1               15
  MALE                5               24
                  vv
clus               N0 N1A N1B N2A N2B N3
  UGT2A3 MUTATED    5   0   1   0   0  0
  UGT2A3 WILD-TYPE 22   3   3   1   2  5
D73V5, multiclass
D73V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  UGT2A3 MUTATED             0       2        1        0        2         0
  UGT2A3 WILD-TYPE           1       1        3        6        2         3
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  UGT2A3 MUTATED           0         0         0          0          1
  UGT2A3 WILD-TYPE         4         2         1          1          5
                  vv
clus               STAGE IIIC STAGE IV
  UGT2A3 MUTATED            0        0
  UGT2A3 WILD-TYPE          6        1
D73V7, multiclass

Clustering(74) Variable = NDUFA13 MUTATION ANALYSIS
D74V1, survival
                   sevent
clus2                0  1
  NDUFA13 MUTATED    1  2
  NDUFA13 WILD-TYPE  8 11
  NDUFA13 MUTATED NDUFA13 WILD-TYPE 
                3                19 
  NDUFA13 MUTATED NDUFA13 WILD-TYPE 
                2                11 
$`NDUFA13 MUTATED`
TCGA-DA-A3F3 TCGA-EE-A29L TCGA-EE-A2A2 
        7.00         1.08        23.90 

$`NDUFA13 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       11.57         4.27         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
        8.09        25.28         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  NDUFA13 MUTATED NDUFA13 WILD-TYPE 
             1.08              2.43 
  NDUFA13 MUTATED NDUFA13 WILD-TYPE 
            23.90             48.79 
  NDUFA13 MUTATED NDUFA13 WILD-TYPE 
             7.00              9.99 
[1] "1.1 - 23.9 (7.0)"  "2.4 - 48.8 (10.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE"   "NDUFA13 MUTATED" "NDUFA13 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"NDUFA13 WILD-TYPE"   "NDUFA13 MUTATED" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "NDUFA13 MUTATED" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE"   "NDUFA13 MUTATED" "NDUFA13 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"NDUFA13 WILD-TYPE"   "NDUFA13 MUTATED" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "NDUFA13 MUTATED" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE"   "NDUFA13 MUTATED" "NDUFA13 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"NDUFA13 WILD-TYPE"   "NDUFA13 MUTATED" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "NDUFA13 MUTATED" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"NDUFA13 WILD-TYPE" "NDUFA13 WILD-TYPE" 
[1] "hr=" "1.7"
D74V2, continuous
                   vv
clus                DISTANT METASTASIS
  NDUFA13 MUTATED                    0
  NDUFA13 WILD-TYPE                  8
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  NDUFA13 MUTATED                                                                                          0
  NDUFA13 WILD-TYPE                                                                                        9
                   vv
clus                REGIONAL LYMPH NODE
  NDUFA13 MUTATED                     4
  NDUFA13 WILD-TYPE                  24
D74V3, multiclass
                                                                                          clus
vv                                                                                         NDUFA13 MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         NDUFA13 WILD-TYPE
  DISTANT METASTASIS                                                                                       8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 9
  REGIONAL LYMPH NODE                                                                                     24
D74V4, binary
                   cls
clus                 0  1
  NDUFA13 MUTATED    0  4
  NDUFA13 WILD-TYPE 16 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NDUFA13 MUTATED      0    4
  NDUFA13 WILD-TYPE   16   25
        clus
vv       NDUFA13 MUTATED NDUFA13 WILD-TYPE
  FEMALE               0                16
  MALE                 4                25
                   vv
clus                N0 N1A N1B N2A N2B N3
  NDUFA13 MUTATED    1   0   1   0   1  1
  NDUFA13 WILD-TYPE 26   3   3   1   1  4
D74V5, multiclass
D74V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  NDUFA13 MUTATED             0       0        1        0        0         0
  NDUFA13 WILD-TYPE           1       3        3        6        4         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  NDUFA13 MUTATED           0         0         0          0          2
  NDUFA13 WILD-TYPE         4         2         1          1          4
                   vv
clus                STAGE IIIC STAGE IV
  NDUFA13 MUTATED            1        0
  NDUFA13 WILD-TYPE          5        1
D74V7, multiclass

Clustering(75) Variable = ZIM3 MUTATION ANALYSIS
D75V1, survival
                sevent
clus2             0  1
  ZIM3 MUTATED    1  1
  ZIM3 WILD-TYPE  8 12
  ZIM3 MUTATED ZIM3 WILD-TYPE 
             2             20 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
             1             12 
$`ZIM3 MUTATED`
TCGA-D3-A2J8 TCGA-ER-A19N 
        8.38        42.84 

$`ZIM3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        2.43         8.09        25.28        23.90         9.67         3.52 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  ZIM3 MUTATED ZIM3 WILD-TYPE 
          8.38           1.08 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
         42.84          48.79 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
         25.61           9.83 
[1] "8.4 - 42.8 (25.6)" "1.1 - 48.8 (9.8)" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE"   "ZIM3 MUTATED" "ZIM3 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE"   "ZIM3 MUTATED" 
    TCGA-GN-A267     TCGA-GN-A268 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE"   "ZIM3 MUTATED" "ZIM3 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE"   "ZIM3 MUTATED" 
    TCGA-GN-A267     TCGA-GN-A268 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE"   "ZIM3 MUTATED" "ZIM3 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE"   "ZIM3 MUTATED" 
    TCGA-GN-A267     TCGA-GN-A268 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
[1] "Remove cluster labels:" "ZIM3 MUTATED"          
clus
  ZIM3 MUTATED ZIM3 WILD-TYPE 
             2             20 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A3MV     TCGA-DA-A1HV 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X     TCGA-EE-A185 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R     TCGA-EE-A29S 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1     TCGA-EE-A2A2 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-GN-A267     TCGA-GN-A268 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
D75V2, continuous
                vv
clus             DISTANT METASTASIS
  ZIM3 MUTATED                    0
  ZIM3 WILD-TYPE                  8
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ZIM3 MUTATED                                                                                          1
  ZIM3 WILD-TYPE                                                                                        8
                vv
clus             REGIONAL LYMPH NODE
  ZIM3 MUTATED                     3
  ZIM3 WILD-TYPE                  25
D75V3, multiclass
                                                                                          clus
vv                                                                                         ZIM3 MUTATED
  DISTANT METASTASIS                                                                                  0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            1
  REGIONAL LYMPH NODE                                                                                 3
                                                                                          clus
vv                                                                                         ZIM3 WILD-TYPE
  DISTANT METASTASIS                                                                                    8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              8
  REGIONAL LYMPH NODE                                                                                  25
D75V4, binary
                cls
clus              0  1
  ZIM3 MUTATED    1  3
  ZIM3 WILD-TYPE 15 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZIM3 MUTATED      1    3
  ZIM3 WILD-TYPE   15   26
        clus
vv       ZIM3 MUTATED ZIM3 WILD-TYPE
  FEMALE            1             15
  MALE              3             26
                vv
clus             N0 N1A N1B N2A N2B N3
  ZIM3 MUTATED    3   0   0   0   0  0
  ZIM3 WILD-TYPE 24   3   4   1   2  5
D75V5, multiclass
D75V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ZIM3 MUTATED             0       0        1        1        0         0
  ZIM3 WILD-TYPE           1       3        3        5        4         3
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ZIM3 MUTATED           1         0         0          0          0          0
  ZIM3 WILD-TYPE         3         2         1          1          6          6
                vv
clus             STAGE IV
  ZIM3 MUTATED          0
  ZIM3 WILD-TYPE        1
D75V7, multiclass

Clustering(76) Variable = DDX3X MUTATION ANALYSIS
D76V1, survival
                 sevent
clus2              0  1
  DDX3X MUTATED    1  1
  DDX3X WILD-TYPE  8 12
  DDX3X MUTATED DDX3X WILD-TYPE 
              2              20 
  DDX3X MUTATED DDX3X WILD-TYPE 
              1              12 
$`DDX3X MUTATED`
TCGA-D3-A2J8 TCGA-EE-A2A1 
        8.38        25.28 

$`DDX3X WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        2.43         8.09        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  DDX3X MUTATED DDX3X WILD-TYPE 
           8.38            1.08 
  DDX3X MUTATED DDX3X WILD-TYPE 
          25.28           48.79 
  DDX3X MUTATED DDX3X WILD-TYPE 
          16.83            9.83 
[1] "8.4 - 25.3 (16.8)" "1.1 - 48.8 (9.8)" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE"   "DDX3X MUTATED" "DDX3X WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE"   "DDX3X MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE"   "DDX3X MUTATED" "DDX3X WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE"   "DDX3X MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE"   "DDX3X MUTATED" "DDX3X WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE"   "DDX3X MUTATED" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
[1] "Remove cluster labels:" "DDX3X MUTATED"         
clus
  DDX3X MUTATED DDX3X WILD-TYPE 
              2              20 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A3MV      TCGA-DA-A1HV 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
     TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X      TCGA-EE-A185 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
     TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R      TCGA-EE-A29S 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A2      TCGA-EE-A2A5 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
     TCGA-ER-A19D      TCGA-ER-A19N      TCGA-GN-A267      TCGA-GN-A268 
"DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" "DDX3X WILD-TYPE" 
D76V2, continuous
                 vv
clus              DISTANT METASTASIS
  DDX3X MUTATED                    1
  DDX3X WILD-TYPE                  7
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DDX3X MUTATED                                                                                          2
  DDX3X WILD-TYPE                                                                                        7
                 vv
clus              REGIONAL LYMPH NODE
  DDX3X MUTATED                     3
  DDX3X WILD-TYPE                  25
D76V3, multiclass
                                                                                          clus
vv                                                                                         DDX3X MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         DDX3X WILD-TYPE
  DISTANT METASTASIS                                                                                     7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   25
D76V4, binary
                 cls
clus               0  1
  DDX3X MUTATED    1  5
  DDX3X WILD-TYPE 15 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      1    5
  DDX3X WILD-TYPE   15   24
        clus
vv       DDX3X MUTATED DDX3X WILD-TYPE
  FEMALE             1              15
  MALE               5              24
                 vv
clus              N0 N1A N1B N2A N2B N3
  DDX3X MUTATED    4   1   0   0   0  0
  DDX3X WILD-TYPE 23   2   4   1   2  5
D76V5, multiclass
D76V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DDX3X MUTATED             0       0        0        2        1         1
  DDX3X WILD-TYPE           1       3        4        4        3         2
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DDX3X MUTATED           0         0         0          0          1
  DDX3X WILD-TYPE         4         2         1          1          5
                 vv
clus              STAGE IIIC STAGE IV
  DDX3X MUTATED            0        0
  DDX3X WILD-TYPE          6        1
D76V7, multiclass

Clustering(77) Variable = LILRB4 MUTATION ANALYSIS
D77V1, survival
                  sevent
clus2               0  1
  LILRB4 MUTATED    0  2
  LILRB4 WILD-TYPE  9 11
  LILRB4 MUTATED LILRB4 WILD-TYPE 
               2               20 
  LILRB4 MUTATED LILRB4 WILD-TYPE 
               2               11 
$`LILRB4 MUTATED`
TCGA-EE-A185 TCGA-EE-A29V 
        4.27         2.43 

$`LILRB4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        7.00        11.57         1.08         8.12         8.84         9.99 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  LILRB4 MUTATED LILRB4 WILD-TYPE 
            2.43             1.08 
  LILRB4 MUTATED LILRB4 WILD-TYPE 
            4.27            48.79 
  LILRB4 MUTATED LILRB4 WILD-TYPE 
            3.35            10.78 
[1] "2.4 - 4.3 (3.3)"   "1.1 - 48.8 (10.8)"
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
  "LILRB4 MUTATED" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"LILRB4 WILD-TYPE"   "LILRB4 MUTATED" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
  "LILRB4 MUTATED" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"LILRB4 WILD-TYPE"   "LILRB4 MUTATED" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
  "LILRB4 MUTATED" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"LILRB4 WILD-TYPE"   "LILRB4 MUTATED" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
[1] "Remove cluster labels:" "LILRB4 MUTATED"        
clus
  LILRB4 MUTATED LILRB4 WILD-TYPE 
               2               20 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R       TCGA-EE-A29S 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-EE-A29X       TCGA-EE-A2A1       TCGA-EE-A2A2       TCGA-EE-A2A5 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
      TCGA-ER-A19D       TCGA-ER-A19N       TCGA-GN-A267       TCGA-GN-A268 
"LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" "LILRB4 WILD-TYPE" 
D77V2, continuous
                  vv
clus               DISTANT METASTASIS
  LILRB4 MUTATED                    3
  LILRB4 WILD-TYPE                  5
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  LILRB4 MUTATED                                                                                          0
  LILRB4 WILD-TYPE                                                                                        9
                  vv
clus               REGIONAL LYMPH NODE
  LILRB4 MUTATED                     3
  LILRB4 WILD-TYPE                  25
D77V3, multiclass
                                                                                          clus
vv                                                                                         LILRB4 MUTATED
  DISTANT METASTASIS                                                                                    3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              0
  REGIONAL LYMPH NODE                                                                                   3
                                                                                          clus
vv                                                                                         LILRB4 WILD-TYPE
  DISTANT METASTASIS                                                                                      5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                9
  REGIONAL LYMPH NODE                                                                                    25
D77V4, binary
                  cls
clus                0  1
  LILRB4 MUTATED    3  3
  LILRB4 WILD-TYPE 13 26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRB4 MUTATED      3    3
  LILRB4 WILD-TYPE   13   26
        clus
vv       LILRB4 MUTATED LILRB4 WILD-TYPE
  FEMALE              3               13
  MALE                3               26
                  vv
clus               N0 N1A N1B N2A N2B N3
  LILRB4 MUTATED    4   0   1   0   0  1
  LILRB4 WILD-TYPE 23   3   3   1   2  4
D77V5, multiclass
D77V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  LILRB4 MUTATED             1       0        2        0        1         0
  LILRB4 WILD-TYPE           0       3        2        6        3         3
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  LILRB4 MUTATED           0         0         0          0          0
  LILRB4 WILD-TYPE         4         2         1          1          6
                  vv
clus               STAGE IIIC STAGE IV
  LILRB4 MUTATED            2        0
  LILRB4 WILD-TYPE          4        1
D77V7, multiclass

Clustering(78) Variable = TLR4 MUTATION ANALYSIS
D78V1, survival
                sevent
clus2             0  1
  TLR4 MUTATED    1  2
  TLR4 WILD-TYPE  8 11
  TLR4 MUTATED TLR4 WILD-TYPE 
             3             19 
  TLR4 MUTATED TLR4 WILD-TYPE 
             2             11 
$`TLR4 MUTATED`
TCGA-EE-A17X TCGA-EE-A2A5 TCGA-ER-A19N 
       11.57         9.67        42.84 

$`TLR4 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        7.00         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19D TCGA-GN-A267 
        2.43         8.09        25.28        23.90         3.52        16.21 
TCGA-GN-A268 
       15.39 

  TLR4 MUTATED TLR4 WILD-TYPE 
          9.67           1.08 
  TLR4 MUTATED TLR4 WILD-TYPE 
         42.84          48.79 
  TLR4 MUTATED TLR4 WILD-TYPE 
         11.57           8.84 
[1] "9.7 - 42.8 (11.6)" "1.1 - 48.8 (8.8)" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE"   "TLR4 MUTATED" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"TLR4 WILD-TYPE"   "TLR4 MUTATED" "TLR4 WILD-TYPE"   "TLR4 MUTATED" 
    TCGA-GN-A267     TCGA-GN-A268 
"TLR4 WILD-TYPE" "TLR4 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE"   "TLR4 MUTATED" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"TLR4 WILD-TYPE"   "TLR4 MUTATED" "TLR4 WILD-TYPE"   "TLR4 MUTATED" 
    TCGA-GN-A267     TCGA-GN-A268 
"TLR4 WILD-TYPE" "TLR4 WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE"   "TLR4 MUTATED" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" "TLR4 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"TLR4 WILD-TYPE"   "TLR4 MUTATED" "TLR4 WILD-TYPE"   "TLR4 MUTATED" 
    TCGA-GN-A267     TCGA-GN-A268 
"TLR4 WILD-TYPE" "TLR4 WILD-TYPE" 
[1] "hr=" "1.1"
D78V2, continuous
                vv
clus             DISTANT METASTASIS
  TLR4 MUTATED                    0
  TLR4 WILD-TYPE                  8
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  TLR4 MUTATED                                                                                          2
  TLR4 WILD-TYPE                                                                                        7
                vv
clus             REGIONAL LYMPH NODE
  TLR4 MUTATED                     7
  TLR4 WILD-TYPE                  21
D78V3, multiclass
                                                                                          clus
vv                                                                                         TLR4 MUTATED
  DISTANT METASTASIS                                                                                  0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            2
  REGIONAL LYMPH NODE                                                                                 7
                                                                                          clus
vv                                                                                         TLR4 WILD-TYPE
  DISTANT METASTASIS                                                                                    8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              7
  REGIONAL LYMPH NODE                                                                                  21
D78V4, binary
                cls
clus              0  1
  TLR4 MUTATED    1  8
  TLR4 WILD-TYPE 15 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLR4 MUTATED      1    8
  TLR4 WILD-TYPE   15   21
        clus
vv       TLR4 MUTATED TLR4 WILD-TYPE
  FEMALE            1             15
  MALE              8             21
                vv
clus             N0 N1A N1B N2A N2B N3
  TLR4 MUTATED    6   1   0   0   0  0
  TLR4 WILD-TYPE 21   2   4   1   2  5
D78V5, multiclass
D78V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  TLR4 MUTATED             0       1        2        1        2         0
  TLR4 WILD-TYPE           1       2        2        5        2         3
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TLR4 MUTATED           0         0         0          0          1          0
  TLR4 WILD-TYPE         4         2         1          1          5          6
                vv
clus             STAGE IV
  TLR4 MUTATED          0
  TLR4 WILD-TYPE        1
D78V7, multiclass

Clustering(79) Variable = ZNF479 MUTATION ANALYSIS
D79V1, survival
                  sevent
clus2               0  1
  ZNF479 MUTATED    2  0
  ZNF479 WILD-TYPE  7 13
  ZNF479 MUTATED ZNF479 WILD-TYPE 
               2               20 
  ZNF479 MUTATED ZNF479 WILD-TYPE 
               0               13 
$`ZNF479 MUTATED`
TCGA-D3-A3MV TCGA-EE-A2A1 
        5.39        25.28 

$`ZNF479 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        2.43         8.09        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  ZNF479 MUTATED ZNF479 WILD-TYPE 
            5.39             1.08 
  ZNF479 MUTATED ZNF479 WILD-TYPE 
           25.28            48.79 
  ZNF479 MUTATED ZNF479 WILD-TYPE 
          15.335            9.830 
[1] "5.4 - 25.3 (15.3)" "1.1 - 48.8 (9.8)" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE"   "ZNF479 MUTATED" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE"   "ZNF479 MUTATED" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE"   "ZNF479 MUTATED" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE"   "ZNF479 MUTATED" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE"   "ZNF479 MUTATED" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE"   "ZNF479 MUTATED" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
[1] "Remove cluster labels:" "ZNF479 MUTATED"        
clus
  ZNF479 MUTATED ZNF479 WILD-TYPE 
               2               20 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-DA-A1HV 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
      TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X       TCGA-EE-A185 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
      TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R       TCGA-EE-A29S 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A2       TCGA-EE-A2A5 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
      TCGA-ER-A19D       TCGA-ER-A19N       TCGA-GN-A267       TCGA-GN-A268 
"ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" "ZNF479 WILD-TYPE" 
D79V2, continuous
                  vv
clus               DISTANT METASTASIS
  ZNF479 MUTATED                    0
  ZNF479 WILD-TYPE                  8
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ZNF479 MUTATED                                                                                          1
  ZNF479 WILD-TYPE                                                                                        8
                  vv
clus               REGIONAL LYMPH NODE
  ZNF479 MUTATED                     2
  ZNF479 WILD-TYPE                  26
D79V3, multiclass
                                                                                          clus
vv                                                                                         ZNF479 MUTATED
  DISTANT METASTASIS                                                                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   2
                                                                                          clus
vv                                                                                         ZNF479 WILD-TYPE
  DISTANT METASTASIS                                                                                      8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    26
D79V4, binary
                  cls
clus                0  1
  ZNF479 MUTATED    1  2
  ZNF479 WILD-TYPE 15 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF479 MUTATED      1    2
  ZNF479 WILD-TYPE   15   27
        clus
vv       ZNF479 MUTATED ZNF479 WILD-TYPE
  FEMALE              1               15
  MALE                2               27
                  vv
clus               N0 N1A N1B N2A N2B N3
  ZNF479 MUTATED    2   0   0   1   0  0
  ZNF479 WILD-TYPE 25   3   4   0   2  5
D79V5, multiclass
D79V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ZNF479 MUTATED             0       0        0        1        1         0
  ZNF479 WILD-TYPE           1       3        4        5        3         3
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ZNF479 MUTATED           0         0         0          0          1
  ZNF479 WILD-TYPE         4         2         1          1          5
                  vv
clus               STAGE IIIC STAGE IV
  ZNF479 MUTATED            0        0
  ZNF479 WILD-TYPE          6        1
D79V7, multiclass

Clustering(80) Variable = GABRG1 MUTATION ANALYSIS
D80V1, survival
                  sevent
clus2               0  1
  GABRG1 MUTATED    2  0
  GABRG1 WILD-TYPE  7 13
  GABRG1 MUTATED GABRG1 WILD-TYPE 
               2               20 
  GABRG1 MUTATED GABRG1 WILD-TYPE 
               0               13 
$`GABRG1 MUTATED`
TCGA-DA-A1HV TCGA-EE-A29S 
       48.79         9.99 

$`GABRG1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       11.57         4.27         1.08         8.12         8.84         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  GABRG1 MUTATED GABRG1 WILD-TYPE 
            9.99             1.08 
  GABRG1 MUTATED GABRG1 WILD-TYPE 
           48.79            42.84 
  GABRG1 MUTATED GABRG1 WILD-TYPE 
          29.390            9.255 
[1] "10.0 - 48.8 (29.4)" "1.1 - 42.8 (9.3)"  
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "GABRG1 MUTATED" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "GABRG1 MUTATED" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "GABRG1 MUTATED" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "GABRG1 MUTATED" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "GABRG1 MUTATED" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
  "GABRG1 MUTATED" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
[1] "Remove cluster labels:" "GABRG1 MUTATED"        
clus
  GABRG1 MUTATED GABRG1 WILD-TYPE 
               2               20 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X       TCGA-EE-A185 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R       TCGA-EE-A29V 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-EE-A29X       TCGA-EE-A2A1       TCGA-EE-A2A2       TCGA-EE-A2A5 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
      TCGA-ER-A19D       TCGA-ER-A19N       TCGA-GN-A267       TCGA-GN-A268 
"GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" "GABRG1 WILD-TYPE" 
D80V2, continuous
                  vv
clus               DISTANT METASTASIS
  GABRG1 MUTATED                    0
  GABRG1 WILD-TYPE                  8
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  GABRG1 MUTATED                                                                                          0
  GABRG1 WILD-TYPE                                                                                        9
                  vv
clus               REGIONAL LYMPH NODE
  GABRG1 MUTATED                     3
  GABRG1 WILD-TYPE                  25
D80V3, multiclass
                                                                                          clus
vv                                                                                         GABRG1 MUTATED
  DISTANT METASTASIS                                                                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              0
  REGIONAL LYMPH NODE                                                                                   3
                                                                                          clus
vv                                                                                         GABRG1 WILD-TYPE
  DISTANT METASTASIS                                                                                      8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                9
  REGIONAL LYMPH NODE                                                                                    25
D80V4, binary
                  cls
clus                0  1
  GABRG1 MUTATED    1  2
  GABRG1 WILD-TYPE 15 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRG1 MUTATED      1    2
  GABRG1 WILD-TYPE   15   27
        clus
vv       GABRG1 MUTATED GABRG1 WILD-TYPE
  FEMALE              1               15
  MALE                2               27
                  vv
clus               N0 N1A N1B N2A N2B N3
  GABRG1 MUTATED    2   0   0   0   1  0
  GABRG1 WILD-TYPE 25   3   4   1   1  5
D80V5, multiclass
D80V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  GABRG1 MUTATED             0       0        0        0        1         1
  GABRG1 WILD-TYPE           1       3        4        6        3         2
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  GABRG1 MUTATED           0         0         0          0          1
  GABRG1 WILD-TYPE         4         2         1          1          5
                  vv
clus               STAGE IIIC STAGE IV
  GABRG1 MUTATED            0        0
  GABRG1 WILD-TYPE          6        1
D80V7, multiclass

Clustering(81) Variable = OR1N2 MUTATION ANALYSIS
D81V1, survival
                 sevent
clus2              0  1
  OR1N2 MUTATED    1  1
  OR1N2 WILD-TYPE  8 12
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              2              20 
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              1              12 
$`OR1N2 MUTATED`
TCGA-D3-A2J8 TCGA-EE-A29S 
        8.38         9.99 

$`OR1N2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       11.57         4.27         1.08         8.12         8.84         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  OR1N2 MUTATED OR1N2 WILD-TYPE 
           8.38            1.08 
  OR1N2 MUTATED OR1N2 WILD-TYPE 
           9.99           48.79 
  OR1N2 MUTATED OR1N2 WILD-TYPE 
          9.185          10.620 
[1] "8.4 - 10.0 (9.2)"  "1.1 - 48.8 (10.6)"
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE"   "OR1N2 MUTATED" "OR1N2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "OR1N2 MUTATED" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE"   "OR1N2 MUTATED" "OR1N2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "OR1N2 MUTATED" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE"   "OR1N2 MUTATED" "OR1N2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "OR1N2 MUTATED" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
[1] "Remove cluster labels:" "OR1N2 MUTATED"         
clus
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              2              20 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A3MV      TCGA-DA-A1HV 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X      TCGA-EE-A185 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R      TCGA-EE-A29V 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-EE-A29X      TCGA-EE-A2A1      TCGA-EE-A2A2      TCGA-EE-A2A5 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-ER-A19D      TCGA-ER-A19N      TCGA-GN-A267      TCGA-GN-A268 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
D81V2, continuous
                 vv
clus              DISTANT METASTASIS
  OR1N2 MUTATED                    1
  OR1N2 WILD-TYPE                  7
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  OR1N2 MUTATED                                                                                          0
  OR1N2 WILD-TYPE                                                                                        9
                 vv
clus              REGIONAL LYMPH NODE
  OR1N2 MUTATED                     5
  OR1N2 WILD-TYPE                  23
D81V3, multiclass
                                                                                          clus
vv                                                                                         OR1N2 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
  REGIONAL LYMPH NODE                                                                                  5
                                                                                          clus
vv                                                                                         OR1N2 WILD-TYPE
  DISTANT METASTASIS                                                                                     7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               9
  REGIONAL LYMPH NODE                                                                                   23
D81V4, binary
                 cls
clus               0  1
  OR1N2 MUTATED    1  5
  OR1N2 WILD-TYPE 15 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1N2 MUTATED      1    5
  OR1N2 WILD-TYPE   15   24
        clus
vv       OR1N2 MUTATED OR1N2 WILD-TYPE
  FEMALE             1              15
  MALE               5              24
                 vv
clus              N0 N1A N1B N2A N2B N3
  OR1N2 MUTATED    5   0   1   0   0  0
  OR1N2 WILD-TYPE 22   3   3   1   2  5
D81V5, multiclass
D81V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  OR1N2 MUTATED             0       1        1        1        1         1
  OR1N2 WILD-TYPE           1       2        3        5        3         2
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  OR1N2 MUTATED           0         0         1          0          0
  OR1N2 WILD-TYPE         4         2         0          1          6
                 vv
clus              STAGE IIIC STAGE IV
  OR1N2 MUTATED            0        0
  OR1N2 WILD-TYPE          6        1
D81V7, multiclass

Clustering(82) Variable = HHLA2 MUTATION ANALYSIS
D82V1, survival
                 sevent
clus2              0  1
  HHLA2 MUTATED    0  2
  HHLA2 WILD-TYPE  9 11
  HHLA2 MUTATED HHLA2 WILD-TYPE 
              2              20 
  HHLA2 MUTATED HHLA2 WILD-TYPE 
              2              11 
$`HHLA2 MUTATED`
TCGA-D3-A2J8 TCGA-EE-A29V 
        8.38         2.43 

$`HHLA2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  HHLA2 MUTATED HHLA2 WILD-TYPE 
           2.43            1.08 
  HHLA2 MUTATED HHLA2 WILD-TYPE 
           8.38           48.79 
  HHLA2 MUTATED HHLA2 WILD-TYPE 
          5.405          10.780 
[1] "2.4 - 8.4 (5.4)"   "1.1 - 48.8 (10.8)"
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE"   "HHLA2 MUTATED" "HHLA2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"HHLA2 WILD-TYPE"   "HHLA2 MUTATED" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE"   "HHLA2 MUTATED" "HHLA2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"HHLA2 WILD-TYPE"   "HHLA2 MUTATED" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE"   "HHLA2 MUTATED" "HHLA2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"HHLA2 WILD-TYPE"   "HHLA2 MUTATED" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
[1] "Remove cluster labels:" "HHLA2 MUTATED"         
clus
  HHLA2 MUTATED HHLA2 WILD-TYPE 
              2              20 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A3MV      TCGA-DA-A1HV 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X      TCGA-EE-A185 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R      TCGA-EE-A29S 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-EE-A29X      TCGA-EE-A2A1      TCGA-EE-A2A2      TCGA-EE-A2A5 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
     TCGA-ER-A19D      TCGA-ER-A19N      TCGA-GN-A267      TCGA-GN-A268 
"HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" "HHLA2 WILD-TYPE" 
D82V2, continuous
                 vv
clus              DISTANT METASTASIS
  HHLA2 MUTATED                    2
  HHLA2 WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  HHLA2 MUTATED                                                                                          0
  HHLA2 WILD-TYPE                                                                                        9
                 vv
clus              REGIONAL LYMPH NODE
  HHLA2 MUTATED                     2
  HHLA2 WILD-TYPE                  26
D82V3, multiclass
                                                                                          clus
vv                                                                                         HHLA2 MUTATED
  DISTANT METASTASIS                                                                                   2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
  REGIONAL LYMPH NODE                                                                                  2
                                                                                          clus
vv                                                                                         HHLA2 WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               9
  REGIONAL LYMPH NODE                                                                                   26
D82V4, binary
                 cls
clus               0  1
  HHLA2 MUTATED    0  4
  HHLA2 WILD-TYPE 16 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HHLA2 MUTATED      0    4
  HHLA2 WILD-TYPE   16   25
        clus
vv       HHLA2 MUTATED HHLA2 WILD-TYPE
  FEMALE             0              16
  MALE               4              25
                 vv
clus              N0 N1A N1B N2A N2B N3
  HHLA2 MUTATED    3   0   1   0   0  0
  HHLA2 WILD-TYPE 24   3   3   1   2  5
D82V5, multiclass
D82V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  HHLA2 MUTATED             0       1        0        1        0         0
  HHLA2 WILD-TYPE           1       2        4        5        4         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  HHLA2 MUTATED           0         1         0          0          0
  HHLA2 WILD-TYPE         4         1         1          1          6
                 vv
clus              STAGE IIIC STAGE IV
  HHLA2 MUTATED            1        0
  HHLA2 WILD-TYPE          5        1
D82V7, multiclass

Clustering(83) Variable = SYCE1 MUTATION ANALYSIS
D83V1, survival
                 sevent
clus2              0  1
  SYCE1 MUTATED    1  0
  SYCE1 WILD-TYPE  8 13
  SYCE1 MUTATED SYCE1 WILD-TYPE 
              1              21 
  SYCE1 MUTATED SYCE1 WILD-TYPE 
              0              13 
$`SYCE1 MUTATED`
TCGA-EE-A2A2 
        23.9 

$`SYCE1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
        7.00        11.57         4.27         1.08         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D 
        9.99         2.43         8.09        25.28         9.67         3.52 
TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       42.84        16.21        15.39 

  SYCE1 MUTATED SYCE1 WILD-TYPE 
          23.90            1.08 
  SYCE1 MUTATED SYCE1 WILD-TYPE 
          23.90           48.79 
  SYCE1 MUTATED SYCE1 WILD-TYPE 
          23.90            9.67 
[1] "23.9 - 23.9 (23.9)" "1.1 - 48.8 (9.7)"  
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "SYCE1 MUTATED" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "SYCE1 MUTATED" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "SYCE1 MUTATED" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
[1] "Remove cluster labels:" "SYCE1 MUTATED"         
clus
  SYCE1 MUTATED SYCE1 WILD-TYPE 
              1              21 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N      TCGA-GN-A267 
"SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" "SYCE1 WILD-TYPE" 
     TCGA-GN-A268 
"SYCE1 WILD-TYPE" 
D83V2, continuous
                 vv
clus              DISTANT METASTASIS
  SYCE1 MUTATED                    2
  SYCE1 WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  SYCE1 MUTATED                                                                                          0
  SYCE1 WILD-TYPE                                                                                        9
                 vv
clus              REGIONAL LYMPH NODE
  SYCE1 MUTATED                     2
  SYCE1 WILD-TYPE                  26
D83V3, multiclass
                                                                                          clus
vv                                                                                         SYCE1 MUTATED
  DISTANT METASTASIS                                                                                   2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
  REGIONAL LYMPH NODE                                                                                  2
                                                                                          clus
vv                                                                                         SYCE1 WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               9
  REGIONAL LYMPH NODE                                                                                   26
D83V4, binary
                 cls
clus               0  1
  SYCE1 MUTATED    1  3
  SYCE1 WILD-TYPE 15 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCE1 MUTATED      1    3
  SYCE1 WILD-TYPE   15   26
        clus
vv       SYCE1 MUTATED SYCE1 WILD-TYPE
  FEMALE             1              15
  MALE               3              26
                 vv
clus              N0 N1A N1B N2A N2B N3
  SYCE1 MUTATED    1   0   2   0   0  0
  SYCE1 WILD-TYPE 26   3   2   1   2  5
D83V5, multiclass
D83V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  SYCE1 MUTATED             0       1        0        0        0         0
  SYCE1 WILD-TYPE           1       2        4        6        4         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  SYCE1 MUTATED           0         0         1          0          1
  SYCE1 WILD-TYPE         4         2         0          1          5
                 vv
clus              STAGE IIIC STAGE IV
  SYCE1 MUTATED            0        0
  SYCE1 WILD-TYPE          6        1
D83V7, multiclass

Clustering(84) Variable = RGPD3 MUTATION ANALYSIS
D84V1, survival
                 sevent
clus2              0  1
  RGPD3 MUTATED    1  2
  RGPD3 WILD-TYPE  8 11
  RGPD3 MUTATED RGPD3 WILD-TYPE 
              3              19 
  RGPD3 MUTATED RGPD3 WILD-TYPE 
              2              11 
$`RGPD3 MUTATED`
TCGA-D3-A1Q8 TCGA-EE-A29L TCGA-EE-A29S 
       28.08         1.08         9.99 

$`RGPD3 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47         8.38         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29X 
       11.57         4.27         8.12         8.84         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
       25.28        23.90         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  RGPD3 MUTATED RGPD3 WILD-TYPE 
           1.08            2.43 
  RGPD3 MUTATED RGPD3 WILD-TYPE 
          28.08           48.79 
  RGPD3 MUTATED RGPD3 WILD-TYPE 
           9.99            9.67 
[1] "1.1 - 28.1 (10.0)" "2.4 - 48.8 (9.7)" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"RGPD3 WILD-TYPE"   "RGPD3 MUTATED" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"RGPD3 WILD-TYPE"   "RGPD3 MUTATED" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "RGPD3 MUTATED" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"RGPD3 WILD-TYPE"   "RGPD3 MUTATED" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"RGPD3 WILD-TYPE"   "RGPD3 MUTATED" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "RGPD3 MUTATED" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"RGPD3 WILD-TYPE"   "RGPD3 MUTATED" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"RGPD3 WILD-TYPE"   "RGPD3 MUTATED" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "RGPD3 MUTATED" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"RGPD3 WILD-TYPE" "RGPD3 WILD-TYPE" 
[1] "hr=" "1.2"
D84V2, continuous
                 vv
clus              DISTANT METASTASIS
  RGPD3 MUTATED                    2
  RGPD3 WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  RGPD3 MUTATED                                                                                          1
  RGPD3 WILD-TYPE                                                                                        8
                 vv
clus              REGIONAL LYMPH NODE
  RGPD3 MUTATED                     6
  RGPD3 WILD-TYPE                  22
D84V3, multiclass
                                                                                          clus
vv                                                                                         RGPD3 MUTATED
  DISTANT METASTASIS                                                                                   2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  6
                                                                                          clus
vv                                                                                         RGPD3 WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               8
  REGIONAL LYMPH NODE                                                                                   22
D84V4, binary
                 cls
clus               0  1
  RGPD3 MUTATED    2  7
  RGPD3 WILD-TYPE 14 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD3 MUTATED      2    7
  RGPD3 WILD-TYPE   14   22
        clus
vv       RGPD3 MUTATED RGPD3 WILD-TYPE
  FEMALE             2              14
  MALE               7              22
                 vv
clus              N0 N1A N1B N2A N2B N3
  RGPD3 MUTATED    5   1   0   0   0  2
  RGPD3 WILD-TYPE 22   2   4   1   2  3
D84V5, multiclass
D84V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  RGPD3 MUTATED             1       0        1        0        1         1
  RGPD3 WILD-TYPE           0       3        3        6        3         2
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  RGPD3 MUTATED           1         0         0          0          1
  RGPD3 WILD-TYPE         3         2         1          1          5
                 vv
clus              STAGE IIIC STAGE IV
  RGPD3 MUTATED            1        1
  RGPD3 WILD-TYPE          5        0
D84V7, multiclass

Clustering(85) Variable = CDH10 MUTATION ANALYSIS
D85V1, survival
                 sevent
clus2             0 1
  CDH10 MUTATED   1 5
  CDH10 WILD-TYPE 8 8
  CDH10 MUTATED CDH10 WILD-TYPE 
              6              16 
  CDH10 MUTATED CDH10 WILD-TYPE 
              5               8 
$`CDH10 MUTATED`
TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A29X TCGA-EE-A2A5 
        8.38        48.79         7.00        11.57         8.09         9.67 

$`CDH10 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-EE-A185 TCGA-EE-A29L 
       16.47        28.08         5.39        39.19         4.27         1.08 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.12         8.84         9.99         2.43        25.28        23.90 
TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
        3.52        42.84        16.21        15.39 

  CDH10 MUTATED CDH10 WILD-TYPE 
           7.00            1.08 
  CDH10 MUTATED CDH10 WILD-TYPE 
          48.79           42.84 
  CDH10 MUTATED CDH10 WILD-TYPE 
          9.025          12.690 
[1] "7.0 - 48.8 (9.0)"  "1.1 - 42.8 (12.7)"
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"CDH10 WILD-TYPE" "CDH10 WILD-TYPE"   "CDH10 MUTATED" "CDH10 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "CDH10 MUTATED" "CDH10 WILD-TYPE"   "CDH10 MUTATED"   "CDH10 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"CDH10 WILD-TYPE" "CDH10 WILD-TYPE" "CDH10 WILD-TYPE" "CDH10 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"CDH10 WILD-TYPE" "CDH10 WILD-TYPE"   "CDH10 MUTATED" "CDH10 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"CDH10 WILD-TYPE"   "CDH10 MUTATED" "CDH10 WILD-TYPE" "CDH10 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"CDH10 WILD-TYPE" "CDH10 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"CDH10 WILD-TYPE" "CDH10 WILD-TYPE"   "CDH10 MUTATED" "CDH10 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "CDH10 MUTATED" "CDH10 WILD-TYPE"   "CDH10 MUTATED"   "CDH10 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"CDH10 WILD-TYPE" "CDH10 WILD-TYPE" "CDH10 WILD-TYPE" "CDH10 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"CDH10 WILD-TYPE" "CDH10 WILD-TYPE"   "CDH10 MUTATED" "CDH10 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"CDH10 WILD-TYPE"   "CDH10 MUTATED" "CDH10 WILD-TYPE" "CDH10 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"CDH10 WILD-TYPE" "CDH10 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"CDH10 WILD-TYPE" "CDH10 WILD-TYPE"   "CDH10 MUTATED" "CDH10 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "CDH10 MUTATED" "CDH10 WILD-TYPE"   "CDH10 MUTATED"   "CDH10 MUTATED" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"CDH10 WILD-TYPE" "CDH10 WILD-TYPE" "CDH10 WILD-TYPE" "CDH10 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"CDH10 WILD-TYPE" "CDH10 WILD-TYPE"   "CDH10 MUTATED" "CDH10 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"CDH10 WILD-TYPE"   "CDH10 MUTATED" "CDH10 WILD-TYPE" "CDH10 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"CDH10 WILD-TYPE" "CDH10 WILD-TYPE" 
[1] "hr=" "2"  
D85V2, continuous
                 vv
clus              DISTANT METASTASIS
  CDH10 MUTATED                    2
  CDH10 WILD-TYPE                  6
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CDH10 MUTATED                                                                                          1
  CDH10 WILD-TYPE                                                                                        8
                 vv
clus              REGIONAL LYMPH NODE
  CDH10 MUTATED                     7
  CDH10 WILD-TYPE                  21
D85V3, multiclass
                                                                                          clus
vv                                                                                         CDH10 MUTATED
  DISTANT METASTASIS                                                                                   2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  7
                                                                                          clus
vv                                                                                         CDH10 WILD-TYPE
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               8
  REGIONAL LYMPH NODE                                                                                   21
D85V4, binary
                 cls
clus               0  1
  CDH10 MUTATED    4  6
  CDH10 WILD-TYPE 12 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH10 MUTATED      4    6
  CDH10 WILD-TYPE   12   23
        clus
vv       CDH10 MUTATED CDH10 WILD-TYPE
  FEMALE             4              12
  MALE               6              23
                 vv
clus              N0 N1A N1B N2A N2B N3
  CDH10 MUTATED    7   0   0   0   2  0
  CDH10 WILD-TYPE 20   3   4   1   0  5
D85V5, multiclass
D85V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CDH10 MUTATED             1       1        1        3        1         0
  CDH10 WILD-TYPE           0       2        3        3        3         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CDH10 MUTATED           0         0         0          0          2
  CDH10 WILD-TYPE         4         2         1          1          4
                 vv
clus              STAGE IIIC STAGE IV
  CDH10 MUTATED            0        0
  CDH10 WILD-TYPE          6        1
D85V7, multiclass

Clustering(86) Variable = C6ORF105 MUTATION ANALYSIS
D86V1, survival
                    sevent
clus2                 0  1
  C6ORF105 MUTATED    2  0
  C6ORF105 WILD-TYPE  7 13
  C6ORF105 MUTATED C6ORF105 WILD-TYPE 
                 2                 20 
  C6ORF105 MUTATED C6ORF105 WILD-TYPE 
                 0                 13 
$`C6ORF105 MUTATED`
TCGA-DA-A1HV TCGA-EE-A29S 
       48.79         9.99 

$`C6ORF105 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       11.57         4.27         1.08         8.12         8.84         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  C6ORF105 MUTATED C6ORF105 WILD-TYPE 
              9.99               1.08 
  C6ORF105 MUTATED C6ORF105 WILD-TYPE 
             48.79              42.84 
  C6ORF105 MUTATED C6ORF105 WILD-TYPE 
            29.390              9.255 
[1] "10.0 - 48.8 (29.4)" "1.1 - 42.8 (9.3)"  
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"C6ORF105 WILD-TYPE"   "C6ORF105 MUTATED" "C6ORF105 WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
  "C6ORF105 MUTATED" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-GN-A268 
"C6ORF105 WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"C6ORF105 WILD-TYPE"   "C6ORF105 MUTATED" "C6ORF105 WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
  "C6ORF105 MUTATED" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-GN-A268 
"C6ORF105 WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"C6ORF105 WILD-TYPE"   "C6ORF105 MUTATED" "C6ORF105 WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
  "C6ORF105 MUTATED" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-GN-A268 
"C6ORF105 WILD-TYPE" 
[1] "Remove cluster labels:" "C6ORF105 MUTATED"      
clus
  C6ORF105 MUTATED C6ORF105 WILD-TYPE 
                 2                 20 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1I1         TCGA-DA-A3F3 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A185         TCGA-EE-A29L 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29V 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A1         TCGA-EE-A2A2 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-EE-A2A5         TCGA-ER-A19D         TCGA-ER-A19N 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"C6ORF105 WILD-TYPE" "C6ORF105 WILD-TYPE" 
D86V2, continuous
                    vv
clus                 DISTANT METASTASIS
  C6ORF105 MUTATED                    0
  C6ORF105 WILD-TYPE                  8
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  C6ORF105 MUTATED                                                                                          1
  C6ORF105 WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  C6ORF105 MUTATED                     3
  C6ORF105 WILD-TYPE                  25
D86V3, multiclass
                                                                                          clus
vv                                                                                         C6ORF105 MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         C6ORF105 WILD-TYPE
  DISTANT METASTASIS                                                                                        8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      25
D86V4, binary
                    cls
clus                  0  1
  C6ORF105 MUTATED    1  3
  C6ORF105 WILD-TYPE 15 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF105 MUTATED      1    3
  C6ORF105 WILD-TYPE   15   26
        clus
vv       C6ORF105 MUTATED C6ORF105 WILD-TYPE
  FEMALE                1                 15
  MALE                  3                 26
                    vv
clus                 N0 N1A N1B N2A N2B N3
  C6ORF105 MUTATED    1   2   0   0   1  0
  C6ORF105 WILD-TYPE 26   1   4   1   1  5
D86V5, multiclass
D86V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  C6ORF105 MUTATED             0       0        0        0        0         1
  C6ORF105 WILD-TYPE           1       3        4        6        4         2
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  C6ORF105 MUTATED           0         0         0          0          3
  C6ORF105 WILD-TYPE         4         2         1          1          3
                    vv
clus                 STAGE IIIC STAGE IV
  C6ORF105 MUTATED            0        0
  C6ORF105 WILD-TYPE          6        1
D86V7, multiclass

Clustering(87) Variable = FPR2 MUTATION ANALYSIS
D87V1, survival
                sevent
clus2             0  1
  FPR2 MUTATED    0  2
  FPR2 WILD-TYPE  9 11
  FPR2 MUTATED FPR2 WILD-TYPE 
             2             20 
  FPR2 MUTATED FPR2 WILD-TYPE 
             2             11 
$`FPR2 MUTATED`
TCGA-D3-A2J8 TCGA-GN-A268 
        8.38        15.39 

$`FPR2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        2.43         8.09        25.28        23.90         9.67         3.52 
TCGA-ER-A19N TCGA-GN-A267 
       42.84        16.21 

  FPR2 MUTATED FPR2 WILD-TYPE 
          8.38           1.08 
  FPR2 MUTATED FPR2 WILD-TYPE 
         15.39          48.79 
  FPR2 MUTATED FPR2 WILD-TYPE 
        11.885          9.830 
[1] "8.4 - 15.4 (11.9)" "1.1 - 48.8 (9.8)" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE"   "FPR2 MUTATED" "FPR2 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"FPR2 WILD-TYPE"   "FPR2 MUTATED" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE"   "FPR2 MUTATED" "FPR2 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"FPR2 WILD-TYPE"   "FPR2 MUTATED" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE"   "FPR2 MUTATED" "FPR2 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"FPR2 WILD-TYPE"   "FPR2 MUTATED" 
[1] "Remove cluster labels:" "FPR2 MUTATED"          
clus
  FPR2 MUTATED FPR2 WILD-TYPE 
             2             20 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A3MV     TCGA-DA-A1HV 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
    TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X     TCGA-EE-A185 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
    TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R     TCGA-EE-A29S 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
    TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1     TCGA-EE-A2A2 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
    TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N     TCGA-GN-A267 
"FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" "FPR2 WILD-TYPE" 
D87V2, continuous
                vv
clus             DISTANT METASTASIS
  FPR2 MUTATED                    1
  FPR2 WILD-TYPE                  7
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  FPR2 MUTATED                                                                                          0
  FPR2 WILD-TYPE                                                                                        9
                vv
clus             REGIONAL LYMPH NODE
  FPR2 MUTATED                     3
  FPR2 WILD-TYPE                  25
D87V3, multiclass
                                                                                          clus
vv                                                                                         FPR2 MUTATED
  DISTANT METASTASIS                                                                                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            0
  REGIONAL LYMPH NODE                                                                                 3
                                                                                          clus
vv                                                                                         FPR2 WILD-TYPE
  DISTANT METASTASIS                                                                                    7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              9
  REGIONAL LYMPH NODE                                                                                  25
D87V4, binary
                cls
clus              0  1
  FPR2 MUTATED    1  3
  FPR2 WILD-TYPE 15 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  FPR2 MUTATED      1    3
  FPR2 WILD-TYPE   15   26
        clus
vv       FPR2 MUTATED FPR2 WILD-TYPE
  FEMALE            1             15
  MALE              3             26
                vv
clus             N0 N1A N1B N2A N2B N3
  FPR2 MUTATED    4   0   0   0   0  0
  FPR2 WILD-TYPE 23   3   4   1   2  5
D87V5, multiclass
D87V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  FPR2 MUTATED             0       0        0        1        1         0
  FPR2 WILD-TYPE           1       3        4        5        3         3
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  FPR2 MUTATED           1         1         0          0          0          0
  FPR2 WILD-TYPE         3         1         1          1          6          6
                vv
clus             STAGE IV
  FPR2 MUTATED          0
  FPR2 WILD-TYPE        1
D87V7, multiclass

Clustering(88) Variable = UGT1A7 MUTATION ANALYSIS
D88V1, survival
                  sevent
clus2               0  1
  UGT1A7 MUTATED    1  0
  UGT1A7 WILD-TYPE  8 13
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               1               21 
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               0               13 
$`UGT1A7 MUTATED`
TCGA-DA-A1HV 
       48.79 

$`UGT1A7 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        2.43         8.09        25.28        23.90         9.67         3.52 
TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       42.84        16.21        15.39 

  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
           48.79             1.08 
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
           48.79            42.84 
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
           48.79             9.67 
[1] "48.8 - 48.8 (48.8)" "1.1 - 42.8 (9.7)"  
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "UGT1A7 MUTATED" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "UGT1A7 MUTATED" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
  "UGT1A7 MUTATED" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
[1] "Remove cluster labels:" "UGT1A7 MUTATED"        
clus
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               1               21 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X       TCGA-EE-A185 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R       TCGA-EE-A29S 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1       TCGA-EE-A2A2 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N       TCGA-GN-A267 
"UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" "UGT1A7 WILD-TYPE" 
      TCGA-GN-A268 
"UGT1A7 WILD-TYPE" 
D88V2, continuous
                  vv
clus               DISTANT METASTASIS
  UGT1A7 MUTATED                    0
  UGT1A7 WILD-TYPE                  8
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  UGT1A7 MUTATED                                                                                          1
  UGT1A7 WILD-TYPE                                                                                        8
                  vv
clus               REGIONAL LYMPH NODE
  UGT1A7 MUTATED                     2
  UGT1A7 WILD-TYPE                  26
D88V3, multiclass
                                                                                          clus
vv                                                                                         UGT1A7 MUTATED
  DISTANT METASTASIS                                                                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   2
                                                                                          clus
vv                                                                                         UGT1A7 WILD-TYPE
  DISTANT METASTASIS                                                                                      8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    26
D88V4, binary
                  cls
clus                0  1
  UGT1A7 MUTATED    1  2
  UGT1A7 WILD-TYPE 15 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A7 MUTATED      1    2
  UGT1A7 WILD-TYPE   15   27
        clus
vv       UGT1A7 MUTATED UGT1A7 WILD-TYPE
  FEMALE              1               15
  MALE                2               27
                  vv
clus               N0 N1A N1B N2A N2B N3
  UGT1A7 MUTATED    2   0   0   0   1  0
  UGT1A7 WILD-TYPE 25   3   4   1   1  5
D88V5, multiclass
D88V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  UGT1A7 MUTATED             0       0        0        0        1         1
  UGT1A7 WILD-TYPE           1       3        4        6        3         2
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  UGT1A7 MUTATED           0         0         0          0          1
  UGT1A7 WILD-TYPE         4         2         1          1          5
                  vv
clus               STAGE IIIC STAGE IV
  UGT1A7 MUTATED            0        0
  UGT1A7 WILD-TYPE          6        1
D88V7, multiclass

Clustering(89) Variable = JAKMIP1 MUTATION ANALYSIS
D89V1, survival
                   sevent
clus2                0  1
  JAKMIP1 MUTATED    0  2
  JAKMIP1 WILD-TYPE  9 11
  JAKMIP1 MUTATED JAKMIP1 WILD-TYPE 
                2                20 
  JAKMIP1 MUTATED JAKMIP1 WILD-TYPE 
                2                11 
$`JAKMIP1 MUTATED`
TCGA-D3-A1Q8 TCGA-ER-A19D 
       28.08         3.52 

$`JAKMIP1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47         8.38         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19N 
        2.43         8.09        25.28        23.90         9.67        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  JAKMIP1 MUTATED JAKMIP1 WILD-TYPE 
             3.52              1.08 
  JAKMIP1 MUTATED JAKMIP1 WILD-TYPE 
            28.08             48.79 
  JAKMIP1 MUTATED JAKMIP1 WILD-TYPE 
            15.80              9.83 
[1] "3.5 - 28.1 (15.8)" "1.1 - 48.8 (9.8)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"JAKMIP1 WILD-TYPE"   "JAKMIP1 MUTATED" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE"   "JAKMIP1 MUTATED" "JAKMIP1 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"JAKMIP1 WILD-TYPE"   "JAKMIP1 MUTATED" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE"   "JAKMIP1 MUTATED" "JAKMIP1 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"JAKMIP1 WILD-TYPE"   "JAKMIP1 MUTATED" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE"   "JAKMIP1 MUTATED" "JAKMIP1 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
[1] "Remove cluster labels:" "JAKMIP1 MUTATED"       
clus
  JAKMIP1 MUTATED JAKMIP1 WILD-TYPE 
                2                20 
       TCGA-D3-A1Q1        TCGA-D3-A2J8        TCGA-D3-A3MV        TCGA-DA-A1HV 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X        TCGA-EE-A185 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1        TCGA-EE-A2A2 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-ER-A19N        TCGA-GN-A267        TCGA-GN-A268 
"JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" "JAKMIP1 WILD-TYPE" 
D89V2, continuous
                   vv
clus                DISTANT METASTASIS
  JAKMIP1 MUTATED                    1
  JAKMIP1 WILD-TYPE                  7
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  JAKMIP1 MUTATED                                                                                          1
  JAKMIP1 WILD-TYPE                                                                                        8
                   vv
clus                REGIONAL LYMPH NODE
  JAKMIP1 MUTATED                     3
  JAKMIP1 WILD-TYPE                  25
D89V3, multiclass
                                                                                          clus
vv                                                                                         JAKMIP1 MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         JAKMIP1 WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 8
  REGIONAL LYMPH NODE                                                                                     25
D89V4, binary
                   cls
clus                 0  1
  JAKMIP1 MUTATED    1  4
  JAKMIP1 WILD-TYPE 15 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  JAKMIP1 MUTATED      1    4
  JAKMIP1 WILD-TYPE   15   25
        clus
vv       JAKMIP1 MUTATED JAKMIP1 WILD-TYPE
  FEMALE               1                15
  MALE                 4                25
                   vv
clus                N0 N1A N1B N2A N2B N3
  JAKMIP1 MUTATED    4   0   0   0   0  1
  JAKMIP1 WILD-TYPE 23   3   4   1   2  4
D89V5, multiclass
D89V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  JAKMIP1 MUTATED             0       0        0        1        2         0
  JAKMIP1 WILD-TYPE           1       3        4        5        2         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  JAKMIP1 MUTATED           0         1         0          0          0
  JAKMIP1 WILD-TYPE         4         1         1          1          6
                   vv
clus                STAGE IIIC STAGE IV
  JAKMIP1 MUTATED            0        1
  JAKMIP1 WILD-TYPE          6        0
D89V7, multiclass

Clustering(90) Variable = CYLC2 MUTATION ANALYSIS
D90V1, survival
                 sevent
clus2              0  1
  CYLC2 MUTATED    2  0
  CYLC2 WILD-TYPE  7 13
  CYLC2 MUTATED CYLC2 WILD-TYPE 
              2              20 
  CYLC2 MUTATED CYLC2 WILD-TYPE 
              0              13 
$`CYLC2 MUTATED`
TCGA-DA-A1I1 TCGA-EE-A2A2 
       39.19        23.90 

$`CYLC2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        48.79         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        2.43         8.09        25.28         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  CYLC2 MUTATED CYLC2 WILD-TYPE 
          23.90            1.08 
  CYLC2 MUTATED CYLC2 WILD-TYPE 
          39.19           48.79 
  CYLC2 MUTATED CYLC2 WILD-TYPE 
         31.545           9.255 
[1] "23.9 - 39.2 (31.5)" "1.1 - 48.8 (9.3)"  
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"CYLC2 WILD-TYPE"   "CYLC2 MUTATED" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "CYLC2 MUTATED" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"CYLC2 WILD-TYPE"   "CYLC2 MUTATED" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "CYLC2 MUTATED" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"CYLC2 WILD-TYPE"   "CYLC2 MUTATED" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
  "CYLC2 MUTATED" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
[1] "Remove cluster labels:" "CYLC2 MUTATED"         
clus
  CYLC2 MUTATED CYLC2 WILD-TYPE 
              2              20 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A3F3      TCGA-EE-A17X      TCGA-EE-A185 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R      TCGA-EE-A29S 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1      TCGA-EE-A2A5 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
     TCGA-ER-A19D      TCGA-ER-A19N      TCGA-GN-A267      TCGA-GN-A268 
"CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" "CYLC2 WILD-TYPE" 
D90V2, continuous
                 vv
clus              DISTANT METASTASIS
  CYLC2 MUTATED                    1
  CYLC2 WILD-TYPE                  7
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CYLC2 MUTATED                                                                                          1
  CYLC2 WILD-TYPE                                                                                        8
                 vv
clus              REGIONAL LYMPH NODE
  CYLC2 MUTATED                     3
  CYLC2 WILD-TYPE                  25
D90V3, multiclass
                                                                                          clus
vv                                                                                         CYLC2 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         CYLC2 WILD-TYPE
  DISTANT METASTASIS                                                                                     7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               8
  REGIONAL LYMPH NODE                                                                                   25
D90V4, binary
                 cls
clus               0  1
  CYLC2 MUTATED    1  4
  CYLC2 WILD-TYPE 15 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYLC2 MUTATED      1    4
  CYLC2 WILD-TYPE   15   25
        clus
vv       CYLC2 MUTATED CYLC2 WILD-TYPE
  FEMALE             1              15
  MALE               4              25
                 vv
clus              N0 N1A N1B N2A N2B N3
  CYLC2 MUTATED    1   1   1   0   0  1
  CYLC2 WILD-TYPE 26   2   3   1   2  4
D90V5, multiclass
D90V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  CYLC2 MUTATED             0       0        0        0        1         0
  CYLC2 WILD-TYPE           1       3        4        6        3         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  CYLC2 MUTATED           0         0         0          0          2
  CYLC2 WILD-TYPE         4         2         1          1          4
                 vv
clus              STAGE IIIC STAGE IV
  CYLC2 MUTATED            1        0
  CYLC2 WILD-TYPE          5        1
D90V7, multiclass

Clustering(91) Variable = DRGX MUTATION ANALYSIS
D91V1, survival
                sevent
clus2             0  1
  DRGX MUTATED    0  2
  DRGX WILD-TYPE  9 11
  DRGX MUTATED DRGX WILD-TYPE 
             2             20 
  DRGX MUTATED DRGX WILD-TYPE 
             2             11 
$`DRGX MUTATED`
TCGA-EE-A29V TCGA-ER-A19D 
        2.43         3.52 

$`DRGX WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
        7.00        11.57         4.27         1.08         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19N 
        9.99         8.09        25.28        23.90         9.67        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  DRGX MUTATED DRGX WILD-TYPE 
          2.43           1.08 
  DRGX MUTATED DRGX WILD-TYPE 
          3.52          48.79 
  DRGX MUTATED DRGX WILD-TYPE 
         2.975         10.780 
[1] "2.4 - 3.5 (3.0)"   "1.1 - 48.8 (10.8)"
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"DRGX WILD-TYPE"   "DRGX MUTATED" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"DRGX WILD-TYPE" "DRGX WILD-TYPE"   "DRGX MUTATED" "DRGX WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"DRGX WILD-TYPE"   "DRGX MUTATED" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"DRGX WILD-TYPE" "DRGX WILD-TYPE"   "DRGX MUTATED" "DRGX WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"DRGX WILD-TYPE"   "DRGX MUTATED" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"DRGX WILD-TYPE" "DRGX WILD-TYPE"   "DRGX MUTATED" "DRGX WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" 
[1] "Remove cluster labels:" "DRGX MUTATED"          
clus
  DRGX MUTATED DRGX WILD-TYPE 
             2             20 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29X     TCGA-EE-A2A1     TCGA-EE-A2A2 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
    TCGA-EE-A2A5     TCGA-ER-A19N     TCGA-GN-A267     TCGA-GN-A268 
"DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" "DRGX WILD-TYPE" 
D91V2, continuous
                vv
clus             DISTANT METASTASIS
  DRGX MUTATED                    2
  DRGX WILD-TYPE                  6
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DRGX MUTATED                                                                                          1
  DRGX WILD-TYPE                                                                                        8
                vv
clus             REGIONAL LYMPH NODE
  DRGX MUTATED                     3
  DRGX WILD-TYPE                  25
D91V3, multiclass
                                                                                          clus
vv                                                                                         DRGX MUTATED
  DISTANT METASTASIS                                                                                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            1
  REGIONAL LYMPH NODE                                                                                 3
                                                                                          clus
vv                                                                                         DRGX WILD-TYPE
  DISTANT METASTASIS                                                                                    6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              8
  REGIONAL LYMPH NODE                                                                                  25
D91V4, binary
                cls
clus              0  1
  DRGX MUTATED    2  4
  DRGX WILD-TYPE 14 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRGX MUTATED      2    4
  DRGX WILD-TYPE   14   25
        clus
vv       DRGX MUTATED DRGX WILD-TYPE
  FEMALE            2             14
  MALE              4             25
                vv
clus             N0 N1A N1B N2A N2B N3
  DRGX MUTATED    4   1   1   0   0  0
  DRGX WILD-TYPE 23   2   3   1   2  5
D91V5, multiclass
D91V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DRGX MUTATED             1       0        0        1        1         1
  DRGX WILD-TYPE           0       3        4        5        3         2
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DRGX MUTATED           0         0         0          0          1          1
  DRGX WILD-TYPE         4         2         1          1          5          5
                vv
clus             STAGE IV
  DRGX MUTATED          0
  DRGX WILD-TYPE        1
D91V7, multiclass

Clustering(92) Variable = IDH1 MUTATION ANALYSIS
D92V1, survival
                sevent
clus2             0  1
  IDH1 MUTATED    0  1
  IDH1 WILD-TYPE  9 12
  IDH1 MUTATED IDH1 WILD-TYPE 
             1             21 
  IDH1 MUTATED IDH1 WILD-TYPE 
             1             12 
$`IDH1 MUTATED`
TCGA-GN-A268 
       15.39 

$`IDH1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
        7.00        11.57         4.27         1.08         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        9.99         2.43         8.09        25.28        23.90         9.67 
TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
        3.52        42.84        16.21 

  IDH1 MUTATED IDH1 WILD-TYPE 
         15.39           1.08 
  IDH1 MUTATED IDH1 WILD-TYPE 
         15.39          48.79 
  IDH1 MUTATED IDH1 WILD-TYPE 
         15.39           9.67 
[1] "15.4 - 15.4 (15.4)" "1.1 - 48.8 (9.7)"  
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"IDH1 WILD-TYPE"   "IDH1 MUTATED" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"IDH1 WILD-TYPE"   "IDH1 MUTATED" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"IDH1 WILD-TYPE"   "IDH1 MUTATED" 
[1] "Remove cluster labels:" "IDH1 MUTATED"          
clus
  IDH1 MUTATED IDH1 WILD-TYPE 
             1             21 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-GN-A267 
"IDH1 WILD-TYPE" 
D92V2, continuous
                vv
clus             DISTANT METASTASIS
  IDH1 MUTATED                    0
  IDH1 WILD-TYPE                  8
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  IDH1 MUTATED                                                                                          0
  IDH1 WILD-TYPE                                                                                        9
                vv
clus             REGIONAL LYMPH NODE
  IDH1 MUTATED                     3
  IDH1 WILD-TYPE                  25
D92V3, multiclass
                                                                                          clus
vv                                                                                         IDH1 MUTATED
  DISTANT METASTASIS                                                                                  0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            0
  REGIONAL LYMPH NODE                                                                                 3
                                                                                          clus
vv                                                                                         IDH1 WILD-TYPE
  DISTANT METASTASIS                                                                                    8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              9
  REGIONAL LYMPH NODE                                                                                  25
D92V4, binary
                cls
clus              0  1
  IDH1 MUTATED    2  1
  IDH1 WILD-TYPE 14 28
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      2    1
  IDH1 WILD-TYPE   14   28
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  FEMALE            2             14
  MALE              1             28
                vv
clus             N0 N1A N1B N2A N2B N3
  IDH1 MUTATED    3   0   0   0   0  0
  IDH1 WILD-TYPE 24   3   4   1   2  5
D92V5, multiclass
D92V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  IDH1 MUTATED             0       0        1        0        1         0
  IDH1 WILD-TYPE           1       3        3        6        3         3
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  IDH1 MUTATED           1         0         0          0          0          0
  IDH1 WILD-TYPE         3         2         1          1          6          6
                vv
clus             STAGE IV
  IDH1 MUTATED          0
  IDH1 WILD-TYPE        1
D92V7, multiclass

Clustering(93) Variable = ASB5 MUTATION ANALYSIS
D93V1, survival
                sevent
clus2             0  1
  ASB5 MUTATED    0  1
  ASB5 WILD-TYPE  9 12
  ASB5 MUTATED ASB5 WILD-TYPE 
             1             21 
  ASB5 MUTATED ASB5 WILD-TYPE 
             1             12 
$`ASB5 MUTATED`
TCGA-GN-A268 
       15.39 

$`ASB5 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
        7.00        11.57         4.27         1.08         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        9.99         2.43         8.09        25.28        23.90         9.67 
TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
        3.52        42.84        16.21 

  ASB5 MUTATED ASB5 WILD-TYPE 
         15.39           1.08 
  ASB5 MUTATED ASB5 WILD-TYPE 
         15.39          48.79 
  ASB5 MUTATED ASB5 WILD-TYPE 
         15.39           9.67 
[1] "15.4 - 15.4 (15.4)" "1.1 - 48.8 (9.7)"  
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"ASB5 WILD-TYPE"   "ASB5 MUTATED" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"ASB5 WILD-TYPE"   "ASB5 MUTATED" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"ASB5 WILD-TYPE"   "ASB5 MUTATED" 
[1] "Remove cluster labels:" "ASB5 MUTATED"          
clus
  ASB5 MUTATED ASB5 WILD-TYPE 
             1             21 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
"ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" "ASB5 WILD-TYPE" 
    TCGA-GN-A267 
"ASB5 WILD-TYPE" 
D93V2, continuous
                vv
clus             DISTANT METASTASIS
  ASB5 MUTATED                    0
  ASB5 WILD-TYPE                  8
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ASB5 MUTATED                                                                                          1
  ASB5 WILD-TYPE                                                                                        8
                vv
clus             REGIONAL LYMPH NODE
  ASB5 MUTATED                     2
  ASB5 WILD-TYPE                  26
D93V3, multiclass
                                                                                          clus
vv                                                                                         ASB5 MUTATED
  DISTANT METASTASIS                                                                                  0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            1
  REGIONAL LYMPH NODE                                                                                 2
                                                                                          clus
vv                                                                                         ASB5 WILD-TYPE
  DISTANT METASTASIS                                                                                    8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              8
  REGIONAL LYMPH NODE                                                                                  26
D93V4, binary
                cls
clus              0  1
  ASB5 MUTATED    1  2
  ASB5 WILD-TYPE 15 27
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASB5 MUTATED      1    2
  ASB5 WILD-TYPE   15   27
        clus
vv       ASB5 MUTATED ASB5 WILD-TYPE
  FEMALE            1             15
  MALE              2             27
                vv
clus             N0 N1A N1B N2A N2B N3
  ASB5 MUTATED    3   0   0   0   0  0
  ASB5 WILD-TYPE 24   3   4   1   2  5
D93V5, multiclass
D93V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ASB5 MUTATED             0       0        0        0        1         1
  ASB5 WILD-TYPE           1       3        4        6        3         2
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ASB5 MUTATED           1         0         0          0          0          0
  ASB5 WILD-TYPE         3         2         1          1          6          6
                vv
clus             STAGE IV
  ASB5 MUTATED          0
  ASB5 WILD-TYPE        1
D93V7, multiclass

Clustering(94) Variable = COL21A1 MUTATION ANALYSIS
D94V1, survival
                   sevent
clus2                0  1
  COL21A1 MUTATED    2  1
  COL21A1 WILD-TYPE  7 12
  COL21A1 MUTATED COL21A1 WILD-TYPE 
                3                19 
  COL21A1 MUTATED COL21A1 WILD-TYPE 
                1                12 
$`COL21A1 MUTATED`
TCGA-EE-A17X TCGA-EE-A2A1 TCGA-EE-A2A2 
       11.57        25.28        23.90 

$`COL21A1 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        7.00         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
        2.43         8.09         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  COL21A1 MUTATED COL21A1 WILD-TYPE 
            11.57              1.08 
  COL21A1 MUTATED COL21A1 WILD-TYPE 
            25.28             48.79 
  COL21A1 MUTATED COL21A1 WILD-TYPE 
            23.90              8.84 
[1] "11.6 - 25.3 (23.9)" "1.1 - 48.8 (8.8)"  
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE"   "COL21A1 MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE"   "COL21A1 MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "COL21A1 MUTATED" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE"   "COL21A1 MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE"   "COL21A1 MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "COL21A1 MUTATED" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE"   "COL21A1 MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE"   "COL21A1 MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "COL21A1 MUTATED" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"COL21A1 WILD-TYPE" "COL21A1 WILD-TYPE" 
[1] "hr=" "2.9"
D94V2, continuous
                   vv
clus                DISTANT METASTASIS
  COL21A1 MUTATED                    2
  COL21A1 WILD-TYPE                  6
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  COL21A1 MUTATED                                                                                          1
  COL21A1 WILD-TYPE                                                                                        8
                   vv
clus                REGIONAL LYMPH NODE
  COL21A1 MUTATED                     6
  COL21A1 WILD-TYPE                  22
D94V3, multiclass
                                                                                          clus
vv                                                                                         COL21A1 MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    6
                                                                                          clus
vv                                                                                         COL21A1 WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 8
  REGIONAL LYMPH NODE                                                                                     22
D94V4, binary
                   cls
clus                 0  1
  COL21A1 MUTATED    2  7
  COL21A1 WILD-TYPE 14 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL21A1 MUTATED      2    7
  COL21A1 WILD-TYPE   14   22
        clus
vv       COL21A1 MUTATED COL21A1 WILD-TYPE
  FEMALE               2                14
  MALE                 7                22
                   vv
clus                N0 N1A N1B N2A N2B N3
  COL21A1 MUTATED    6   1   2   0   0  0
  COL21A1 WILD-TYPE 21   2   2   1   2  5
D94V5, multiclass
D94V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  COL21A1 MUTATED             0       0        4        1        1         0
  COL21A1 WILD-TYPE           1       3        0        5        3         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  COL21A1 MUTATED           0         0         1          0          2
  COL21A1 WILD-TYPE         4         2         0          1          4
                   vv
clus                STAGE IIIC STAGE IV
  COL21A1 MUTATED            0        0
  COL21A1 WILD-TYPE          6        1
D94V7, multiclass

Clustering(95) Variable = OR4M2 MUTATION ANALYSIS
D95V1, survival
                 sevent
clus2              0  1
  OR4M2 MUTATED    2  1
  OR4M2 WILD-TYPE  7 12
  OR4M2 MUTATED OR4M2 WILD-TYPE 
              3              19 
  OR4M2 MUTATED OR4M2 WILD-TYPE 
              1              12 
$`OR4M2 MUTATED`
TCGA-DA-A1HV TCGA-EE-A29L TCGA-EE-A29S 
       48.79         1.08         9.99 

$`OR4M2 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29X 
       11.57         4.27         8.12         8.84         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
       25.28        23.90         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  OR4M2 MUTATED OR4M2 WILD-TYPE 
           1.08            2.43 
  OR4M2 MUTATED OR4M2 WILD-TYPE 
          48.79           42.84 
  OR4M2 MUTATED OR4M2 WILD-TYPE 
           9.99            9.67 
[1] "1.1 - 48.8 (10.0)" "2.4 - 42.8 (9.7)" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "OR4M2 MUTATED" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"OR4M2 WILD-TYPE"   "OR4M2 MUTATED" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "OR4M2 MUTATED" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "OR4M2 MUTATED" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"OR4M2 WILD-TYPE"   "OR4M2 MUTATED" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "OR4M2 MUTATED" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
  "OR4M2 MUTATED" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
"OR4M2 WILD-TYPE"   "OR4M2 MUTATED" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
  "OR4M2 MUTATED" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"OR4M2 WILD-TYPE" "OR4M2 WILD-TYPE" 
[1] "hr=" "1.8"
D95V2, continuous
                 vv
clus              DISTANT METASTASIS
  OR4M2 MUTATED                    0
  OR4M2 WILD-TYPE                  8
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  OR4M2 MUTATED                                                                                          2
  OR4M2 WILD-TYPE                                                                                        7
                 vv
clus              REGIONAL LYMPH NODE
  OR4M2 MUTATED                     4
  OR4M2 WILD-TYPE                  24
D95V3, multiclass
                                                                                          clus
vv                                                                                         OR4M2 MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             2
  REGIONAL LYMPH NODE                                                                                  4
                                                                                          clus
vv                                                                                         OR4M2 WILD-TYPE
  DISTANT METASTASIS                                                                                     8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   24
D95V4, binary
                 cls
clus               0  1
  OR4M2 MUTATED    2  4
  OR4M2 WILD-TYPE 14 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4M2 MUTATED      2    4
  OR4M2 WILD-TYPE   14   25
        clus
vv       OR4M2 MUTATED OR4M2 WILD-TYPE
  FEMALE             2              14
  MALE               4              25
                 vv
clus              N0 N1A N1B N2A N2B N3
  OR4M2 MUTATED    3   1   0   0   1  1
  OR4M2 WILD-TYPE 24   2   4   1   1  4
D95V5, multiclass
D95V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  OR4M2 MUTATED             0       1        0        0        0         2
  OR4M2 WILD-TYPE           1       2        4        6        4         1
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  OR4M2 MUTATED           0         0         0          0          2
  OR4M2 WILD-TYPE         4         2         1          1          4
                 vv
clus              STAGE IIIC STAGE IV
  OR4M2 MUTATED            1        0
  OR4M2 WILD-TYPE          5        1
D95V7, multiclass

Clustering(96) Variable = ANKRD45 MUTATION ANALYSIS
D96V1, survival
                   sevent
clus2                0  1
  ANKRD45 MUTATED    2  3
  ANKRD45 WILD-TYPE  7 10
  ANKRD45 MUTATED ANKRD45 WILD-TYPE 
                5                17 
  ANKRD45 MUTATED ANKRD45 WILD-TYPE 
                3                10 
$`ANKRD45 MUTATED`
TCGA-DA-A1HV TCGA-EE-A29L TCGA-EE-A29S TCGA-EE-A29V TCGA-GN-A267 
       48.79         1.08         9.99         2.43        16.21 

$`ANKRD45 WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29X TCGA-EE-A2A1 
       11.57         4.27         8.12         8.84         8.09        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A268 
       23.90         9.67         3.52        42.84        15.39 

  ANKRD45 MUTATED ANKRD45 WILD-TYPE 
             1.08              3.52 
  ANKRD45 MUTATED ANKRD45 WILD-TYPE 
            48.79             42.84 
  ANKRD45 MUTATED ANKRD45 WILD-TYPE 
             9.99              9.67 
[1] "1.1 - 48.8 (10.0)" "3.5 - 42.8 (9.7)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "ANKRD45 MUTATED" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"ANKRD45 WILD-TYPE"   "ANKRD45 MUTATED" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "ANKRD45 MUTATED"   "ANKRD45 MUTATED" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
  "ANKRD45 MUTATED" "ANKRD45 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "ANKRD45 MUTATED" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"ANKRD45 WILD-TYPE"   "ANKRD45 MUTATED" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "ANKRD45 MUTATED"   "ANKRD45 MUTATED" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
  "ANKRD45 MUTATED" "ANKRD45 WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "ANKRD45 MUTATED" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"ANKRD45 WILD-TYPE"   "ANKRD45 MUTATED" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "ANKRD45 MUTATED"   "ANKRD45 MUTATED" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" "ANKRD45 WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
  "ANKRD45 MUTATED" "ANKRD45 WILD-TYPE" 
[1] "hr=" "1.2"
D96V2, continuous
                   vv
clus                DISTANT METASTASIS
  ANKRD45 MUTATED                    1
  ANKRD45 WILD-TYPE                  7
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ANKRD45 MUTATED                                                                                          1
  ANKRD45 WILD-TYPE                                                                                        8
                   vv
clus                REGIONAL LYMPH NODE
  ANKRD45 MUTATED                     5
  ANKRD45 WILD-TYPE                  23
D96V3, multiclass
                                                                                          clus
vv                                                                                         ANKRD45 MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         ANKRD45 WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 8
  REGIONAL LYMPH NODE                                                                                     23
D96V4, binary
                   cls
clus                 0  1
  ANKRD45 MUTATED    1  6
  ANKRD45 WILD-TYPE 15 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD45 MUTATED      1    6
  ANKRD45 WILD-TYPE   15   23
        clus
vv       ANKRD45 MUTATED ANKRD45 WILD-TYPE
  FEMALE               1                15
  MALE                 6                23
                   vv
clus                N0 N1A N1B N2A N2B N3
  ANKRD45 MUTATED    1   2   1   0   1  1
  ANKRD45 WILD-TYPE 26   1   3   1   1  4
D96V5, multiclass
D96V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ANKRD45 MUTATED             0       0        0        0        0         1
  ANKRD45 WILD-TYPE           1       3        4        6        4         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ANKRD45 MUTATED           0         0         0          1          2
  ANKRD45 WILD-TYPE         4         2         1          0          4
                   vv
clus                STAGE IIIC STAGE IV
  ANKRD45 MUTATED            2        0
  ANKRD45 WILD-TYPE          4        1
D96V7, multiclass

Clustering(97) Variable = LCE1B MUTATION ANALYSIS
D97V1, survival
                 sevent
clus2              0  1
  LCE1B MUTATED    0  1
  LCE1B WILD-TYPE  9 12
  LCE1B MUTATED LCE1B WILD-TYPE 
              1              21 
  LCE1B MUTATED LCE1B WILD-TYPE 
              1              12 
$`LCE1B MUTATED`
TCGA-EE-A185 
        4.27 

$`LCE1B WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        7.00        11.57         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        2.43         8.09        25.28        23.90         9.67         3.52 
TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       42.84        16.21        15.39 

  LCE1B MUTATED LCE1B WILD-TYPE 
           4.27            1.08 
  LCE1B MUTATED LCE1B WILD-TYPE 
           4.27           48.79 
  LCE1B MUTATED LCE1B WILD-TYPE 
           4.27            9.99 
[1] "4.3 - 4.3 (4.3)"   "1.1 - 48.8 (10.0)"
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
  "LCE1B MUTATED" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
  "LCE1B MUTATED" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-EE-A185      TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R 
  "LCE1B MUTATED" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-EE-A29S      TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-EE-A2A2      TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-GN-A267      TCGA-GN-A268 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
[1] "Remove cluster labels:" "LCE1B MUTATED"         
clus
  LCE1B MUTATED LCE1B WILD-TYPE 
              1              21 
     TCGA-D3-A1Q1      TCGA-D3-A1Q8      TCGA-D3-A2J8      TCGA-D3-A3MV 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-DA-A1HV      TCGA-DA-A1I1      TCGA-DA-A3F3      TCGA-EE-A17X 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-EE-A29L      TCGA-EE-A29Q      TCGA-EE-A29R      TCGA-EE-A29S 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-EE-A29V      TCGA-EE-A29X      TCGA-EE-A2A1      TCGA-EE-A2A2 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-EE-A2A5      TCGA-ER-A19D      TCGA-ER-A19N      TCGA-GN-A267 
"LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" "LCE1B WILD-TYPE" 
     TCGA-GN-A268 
"LCE1B WILD-TYPE" 
D97V2, continuous
                 vv
clus              DISTANT METASTASIS
  LCE1B MUTATED                    0
  LCE1B WILD-TYPE                  8
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  LCE1B MUTATED                                                                                          1
  LCE1B WILD-TYPE                                                                                        8
                 vv
clus              REGIONAL LYMPH NODE
  LCE1B MUTATED                     3
  LCE1B WILD-TYPE                  25
D97V3, multiclass
                                                                                          clus
vv                                                                                         LCE1B MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         LCE1B WILD-TYPE
  DISTANT METASTASIS                                                                                     8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               8
  REGIONAL LYMPH NODE                                                                                   25
D97V4, binary
                 cls
clus               0  1
  LCE1B MUTATED    2  2
  LCE1B WILD-TYPE 14 27
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE1B MUTATED      2    2
  LCE1B WILD-TYPE   14   27
        clus
vv       LCE1B MUTATED LCE1B WILD-TYPE
  FEMALE             2              14
  MALE               2              27
                 vv
clus              N0 N1A N1B N2A N2B N3
  LCE1B MUTATED    2   1   0   0   0  1
  LCE1B WILD-TYPE 25   2   4   1   2  4
D97V5, multiclass
D97V6, continuous
                 vv
clus              I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  LCE1B MUTATED             0       0        1        0        1         0
  LCE1B WILD-TYPE           1       3        3        6        3         3
                 vv
clus              STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  LCE1B MUTATED           0         0         0          0          1
  LCE1B WILD-TYPE         4         2         1          1          5
                 vv
clus              STAGE IIIC STAGE IV
  LCE1B MUTATED            1        0
  LCE1B WILD-TYPE          5        1
D97V7, multiclass

Clustering(98) Variable = MGAM MUTATION ANALYSIS
D98V1, survival
                sevent
clus2            0 1
  MGAM MUTATED   4 4
  MGAM WILD-TYPE 5 9
  MGAM MUTATED MGAM WILD-TYPE 
             8             14 
  MGAM MUTATED MGAM WILD-TYPE 
             4              9 
$`MGAM MUTATED`
TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29V 
       48.79        39.19        11.57         1.08         8.12         2.43 
TCGA-EE-A2A2 TCGA-EE-A2A5 
       23.90         9.67 

$`MGAM WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A3F3 TCGA-EE-A185 
       16.47        28.08         8.38         5.39         7.00         4.27 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A1 TCGA-ER-A19D TCGA-ER-A19N 
        8.84         9.99         8.09        25.28         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  MGAM MUTATED MGAM WILD-TYPE 
          1.08           3.52 
  MGAM MUTATED MGAM WILD-TYPE 
         48.79          42.84 
  MGAM MUTATED MGAM WILD-TYPE 
        10.620          9.415 
[1] "1.1 - 48.8 (10.6)" "3.5 - 42.8 (9.4)" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"MGAM WILD-TYPE" "MGAM WILD-TYPE" "MGAM WILD-TYPE" "MGAM WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "MGAM MUTATED"   "MGAM MUTATED" "MGAM WILD-TYPE"   "MGAM MUTATED" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"MGAM WILD-TYPE"   "MGAM MUTATED"   "MGAM MUTATED" "MGAM WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"MGAM WILD-TYPE"   "MGAM MUTATED" "MGAM WILD-TYPE" "MGAM WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
  "MGAM MUTATED"   "MGAM MUTATED" "MGAM WILD-TYPE" "MGAM WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"MGAM WILD-TYPE" "MGAM WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"MGAM WILD-TYPE" "MGAM WILD-TYPE" "MGAM WILD-TYPE" "MGAM WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "MGAM MUTATED"   "MGAM MUTATED" "MGAM WILD-TYPE"   "MGAM MUTATED" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"MGAM WILD-TYPE"   "MGAM MUTATED"   "MGAM MUTATED" "MGAM WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"MGAM WILD-TYPE"   "MGAM MUTATED" "MGAM WILD-TYPE" "MGAM WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
  "MGAM MUTATED"   "MGAM MUTATED" "MGAM WILD-TYPE" "MGAM WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"MGAM WILD-TYPE" "MGAM WILD-TYPE" 
    TCGA-D3-A1Q1     TCGA-D3-A1Q8     TCGA-D3-A2J8     TCGA-D3-A3MV 
"MGAM WILD-TYPE" "MGAM WILD-TYPE" "MGAM WILD-TYPE" "MGAM WILD-TYPE" 
    TCGA-DA-A1HV     TCGA-DA-A1I1     TCGA-DA-A3F3     TCGA-EE-A17X 
  "MGAM MUTATED"   "MGAM MUTATED" "MGAM WILD-TYPE"   "MGAM MUTATED" 
    TCGA-EE-A185     TCGA-EE-A29L     TCGA-EE-A29Q     TCGA-EE-A29R 
"MGAM WILD-TYPE"   "MGAM MUTATED"   "MGAM MUTATED" "MGAM WILD-TYPE" 
    TCGA-EE-A29S     TCGA-EE-A29V     TCGA-EE-A29X     TCGA-EE-A2A1 
"MGAM WILD-TYPE"   "MGAM MUTATED" "MGAM WILD-TYPE" "MGAM WILD-TYPE" 
    TCGA-EE-A2A2     TCGA-EE-A2A5     TCGA-ER-A19D     TCGA-ER-A19N 
  "MGAM MUTATED"   "MGAM MUTATED" "MGAM WILD-TYPE" "MGAM WILD-TYPE" 
    TCGA-GN-A267     TCGA-GN-A268 
"MGAM WILD-TYPE" "MGAM WILD-TYPE" 
[1] "hr=" "1.3"
D98V2, continuous
                vv
clus             DISTANT METASTASIS
  MGAM MUTATED                    5
  MGAM WILD-TYPE                  3
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  MGAM MUTATED                                                                                          3
  MGAM WILD-TYPE                                                                                        6
                vv
clus             REGIONAL LYMPH NODE
  MGAM MUTATED                    10
  MGAM WILD-TYPE                  18
D98V3, multiclass
                                                                                          clus
vv                                                                                         MGAM MUTATED
  DISTANT METASTASIS                                                                                  5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            3
  REGIONAL LYMPH NODE                                                                                10
                                                                                          clus
vv                                                                                         MGAM WILD-TYPE
  DISTANT METASTASIS                                                                                    3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              6
  REGIONAL LYMPH NODE                                                                                  18
D98V4, binary
                cls
clus              0  1
  MGAM MUTATED    5 13
  MGAM WILD-TYPE 11 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  MGAM MUTATED      5   13
  MGAM WILD-TYPE   11   16
        clus
vv       MGAM MUTATED MGAM WILD-TYPE
  FEMALE            5             11
  MALE             13             16
                vv
clus             N0 N1A N1B N2A N2B N3
  MGAM MUTATED   10   1   2   0   1  2
  MGAM WILD-TYPE 17   2   2   1   1  3
D98V5, multiclass
D98V6, continuous
                vv
clus             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  MGAM MUTATED             1       2        3        1        2         0
  MGAM WILD-TYPE           0       1        1        5        2         3
                vv
clus             STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MGAM MUTATED           1         0         0          0          3          3
  MGAM WILD-TYPE         3         2         1          1          3          3
                vv
clus             STAGE IV
  MGAM MUTATED          0
  MGAM WILD-TYPE        1
D98V7, multiclass

Clustering(99) Variable = ACSM2B MUTATION ANALYSIS
D99V1, survival
                  sevent
clus2               0  1
  ACSM2B MUTATED    0  3
  ACSM2B WILD-TYPE  9 10
  ACSM2B MUTATED ACSM2B WILD-TYPE 
               3               19 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
               3               10 
$`ACSM2B MUTATED`
TCGA-EE-A29L TCGA-EE-A29V TCGA-GN-A267 
        1.08         2.43        16.21 

$`ACSM2B WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        7.00        11.57         4.27         8.12         8.84         9.99 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A268 
       15.39 

  ACSM2B MUTATED ACSM2B WILD-TYPE 
            1.08             3.52 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
           16.21            48.79 
  ACSM2B MUTATED ACSM2B WILD-TYPE 
            2.43             9.99 
[1] "1.1 - 16.2 (2.4)"  "3.5 - 48.8 (10.0)"
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"ACSM2B WILD-TYPE"   "ACSM2B MUTATED" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"ACSM2B WILD-TYPE"   "ACSM2B MUTATED" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
  "ACSM2B MUTATED" "ACSM2B WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"ACSM2B WILD-TYPE"   "ACSM2B MUTATED" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"ACSM2B WILD-TYPE"   "ACSM2B MUTATED" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
  "ACSM2B MUTATED" "ACSM2B WILD-TYPE" 
      TCGA-D3-A1Q1       TCGA-D3-A1Q8       TCGA-D3-A2J8       TCGA-D3-A3MV 
"ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-DA-A1HV       TCGA-DA-A1I1       TCGA-DA-A3F3       TCGA-EE-A17X 
"ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-EE-A185       TCGA-EE-A29L       TCGA-EE-A29Q       TCGA-EE-A29R 
"ACSM2B WILD-TYPE"   "ACSM2B MUTATED" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-EE-A29S       TCGA-EE-A29V       TCGA-EE-A29X       TCGA-EE-A2A1 
"ACSM2B WILD-TYPE"   "ACSM2B MUTATED" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-EE-A2A2       TCGA-EE-A2A5       TCGA-ER-A19D       TCGA-ER-A19N 
"ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" "ACSM2B WILD-TYPE" 
      TCGA-GN-A267       TCGA-GN-A268 
  "ACSM2B MUTATED" "ACSM2B WILD-TYPE" 
[1] "hr=" "4.1"
D99V2, continuous
                  vv
clus               DISTANT METASTASIS
  ACSM2B MUTATED                    2
  ACSM2B WILD-TYPE                  6
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ACSM2B MUTATED                                                                                          1
  ACSM2B WILD-TYPE                                                                                        8
                  vv
clus               REGIONAL LYMPH NODE
  ACSM2B MUTATED                     3
  ACSM2B WILD-TYPE                  25
D99V3, multiclass
                                                                                          clus
vv                                                                                         ACSM2B MUTATED
  DISTANT METASTASIS                                                                                    2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
  REGIONAL LYMPH NODE                                                                                   3
                                                                                          clus
vv                                                                                         ACSM2B WILD-TYPE
  DISTANT METASTASIS                                                                                      6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    25
D99V4, binary
                  cls
clus                0  1
  ACSM2B MUTATED    2  4
  ACSM2B WILD-TYPE 14 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACSM2B MUTATED      2    4
  ACSM2B WILD-TYPE   14   25
        clus
vv       ACSM2B MUTATED ACSM2B WILD-TYPE
  FEMALE              2               14
  MALE                4               25
                  vv
clus               N0 N1A N1B N2A N2B N3
  ACSM2B MUTATED    3   1   1   0   0  1
  ACSM2B WILD-TYPE 24   2   3   1   2  4
D99V5, multiclass
D99V6, continuous
                  vv
clus               I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  ACSM2B MUTATED             1       1        0        0        0         0
  ACSM2B WILD-TYPE           0       2        4        6        4         3
                  vv
clus               STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  ACSM2B MUTATED           0         1         0          1          0
  ACSM2B WILD-TYPE         4         1         1          0          6
                  vv
clus               STAGE IIIC STAGE IV
  ACSM2B MUTATED            2        0
  ACSM2B WILD-TYPE          4        1
D99V7, 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")
