
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_Cluster_mutation_onlysig.3.4048/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_mutation_onlysig.3.4048/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/397681/STAD-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/STAD-TP/3144511/1.GDAC_mergedClustering.Finished/STAD-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=STAD-TP", "-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=STAD-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=308, in cluster file=116, common to both=116
[1]  47 116
[1] "CBWD1 MUTATION ANALYSIS"
[1] 3
  CBWD1 MUTATED CBWD1 WILD-TYPE 
             14             102 
  CBWD1 MUTATED CBWD1 WILD-TYPE 
             14             102 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            14            102 
  KRAS MUTATED KRAS WILD-TYPE 
            14            102 
[1] "PGM5 MUTATION ANALYSIS"
[1] 3
  PGM5 MUTATED PGM5 WILD-TYPE 
            16            100 
  PGM5 MUTATED PGM5 WILD-TYPE 
            16            100 
[1] "RPL22 MUTATION ANALYSIS"
[1] 3
  RPL22 MUTATED RPL22 WILD-TYPE 
              9             107 
  RPL22 MUTATED RPL22 WILD-TYPE 
              9             107 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            52             64 
  TP53 MUTATED TP53 WILD-TYPE 
            52             64 
[1] "TRIM48 MUTATION ANALYSIS"
[1] 3
  TRIM48 MUTATED TRIM48 WILD-TYPE 
              10              106 
  TRIM48 MUTATED TRIM48 WILD-TYPE 
              10              106 
[1] "XPOT MUTATION ANALYSIS"
[1] 3
  XPOT MUTATED XPOT WILD-TYPE 
             6            110 
  XPOT MUTATED XPOT WILD-TYPE 
             6            110 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              24               92 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              24               92 
[1] "ACVR2A MUTATION ANALYSIS"
[1] 3
  ACVR2A MUTATED ACVR2A WILD-TYPE 
              13              103 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
              13              103 
[1] "RHOA MUTATION ANALYSIS"
[1] 3
  RHOA MUTATED RHOA WILD-TYPE 
             7            109 
  RHOA MUTATED RHOA WILD-TYPE 
             7            109 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              22               94 
  ARID1A MUTATED ARID1A WILD-TYPE 
              22               94 
[1] "OR8H3 MUTATION ANALYSIS"
[1] 3
  OR8H3 MUTATED OR8H3 WILD-TYPE 
             10             106 
  OR8H3 MUTATED OR8H3 WILD-TYPE 
             10             106 
[1] "EDNRB MUTATION ANALYSIS"
[1] 3
  EDNRB MUTATED EDNRB WILD-TYPE 
             12             104 
  EDNRB MUTATED EDNRB WILD-TYPE 
             12             104 
[1] "ZNF804B MUTATION ANALYSIS"
[1] 3
  ZNF804B MUTATED ZNF804B WILD-TYPE 
               18                98 
  ZNF804B MUTATED ZNF804B WILD-TYPE 
               18                98 
[1] "IRF2 MUTATION ANALYSIS"
[1] 3
  IRF2 MUTATED IRF2 WILD-TYPE 
             8            108 
  IRF2 MUTATED IRF2 WILD-TYPE 
             8            108 
[1] "IAPP MUTATION ANALYSIS"
[1] 3
  IAPP MUTATED IAPP WILD-TYPE 
             4            112 
  IAPP MUTATED IAPP WILD-TYPE 
             4            112 
[1] "PCDH15 MUTATION ANALYSIS"
[1] 3
  PCDH15 MUTATED PCDH15 WILD-TYPE 
              22               94 
  PCDH15 MUTATED PCDH15 WILD-TYPE 
              22               94 
[1] "SPRYD5 MUTATION ANALYSIS"
[1] 3
  SPRYD5 MUTATED SPRYD5 WILD-TYPE 
               8              108 
  SPRYD5 MUTATED SPRYD5 WILD-TYPE 
               8              108 
[1] "TUSC3 MUTATION ANALYSIS"
[1] 3
  TUSC3 MUTATED TUSC3 WILD-TYPE 
              9             107 
  TUSC3 MUTATED TUSC3 WILD-TYPE 
              9             107 
[1] "FGF22 MUTATION ANALYSIS"
[1] 3
  FGF22 MUTATED FGF22 WILD-TYPE 
              3             113 
  FGF22 MUTATED FGF22 WILD-TYPE 
              3             113 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
              9             107 
  HLA-B MUTATED HLA-B WILD-TYPE 
              9             107 
[1] "PTH2 MUTATION ANALYSIS"
[1] 3
  PTH2 MUTATED PTH2 WILD-TYPE 
             3            113 
  PTH2 MUTATED PTH2 WILD-TYPE 
             3            113 
[1] "C17ORF63 MUTATION ANALYSIS"
[1] 3
  C17ORF63 MUTATED C17ORF63 WILD-TYPE 
                 3                113 
  C17ORF63 MUTATED C17ORF63 WILD-TYPE 
                 3                113 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              7             109 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              7             109 
[1] "POTEG MUTATION ANALYSIS"
[1] 3
  POTEG MUTATED POTEG WILD-TYPE 
              6             110 
  POTEG MUTATED POTEG WILD-TYPE 
              6             110 
[1] "RNF43 MUTATION ANALYSIS"
[1] 3
  RNF43 MUTATED RNF43 WILD-TYPE 
             13             103 
  RNF43 MUTATED RNF43 WILD-TYPE 
             13             103 
[1] "WBSCR17 MUTATION ANALYSIS"
[1] 3
  WBSCR17 MUTATED WBSCR17 WILD-TYPE 
               12               104 
  WBSCR17 MUTATED WBSCR17 WILD-TYPE 
               12               104 
[1] "PHF2 MUTATION ANALYSIS"
[1] 3
  PHF2 MUTATED PHF2 WILD-TYPE 
            12            104 
  PHF2 MUTATED PHF2 WILD-TYPE 
            12            104 
[1] "TPTE MUTATION ANALYSIS"
[1] 3
  TPTE MUTATED TPTE WILD-TYPE 
            14            102 
  TPTE MUTATED TPTE WILD-TYPE 
            14            102 
[1] "CDH1 MUTATION ANALYSIS"
[1] 3
  CDH1 MUTATED CDH1 WILD-TYPE 
            11            105 
  CDH1 MUTATED CDH1 WILD-TYPE 
            11            105 
[1] "CPS1 MUTATION ANALYSIS"
[1] 3
  CPS1 MUTATED CPS1 WILD-TYPE 
            13            103 
  CPS1 MUTATED CPS1 WILD-TYPE 
            13            103 
[1] "INO80E MUTATION ANALYSIS"
[1] 3
  INO80E MUTATED INO80E WILD-TYPE 
               5              111 
  INO80E MUTATED INO80E WILD-TYPE 
               5              111 
[1] "ELF3 MUTATION ANALYSIS"
[1] 3
  ELF3 MUTATED ELF3 WILD-TYPE 
             5            111 
  ELF3 MUTATED ELF3 WILD-TYPE 
             5            111 
[1] "PARK2 MUTATION ANALYSIS"
[1] 3
  PARK2 MUTATED PARK2 WILD-TYPE 
              9             107 
  PARK2 MUTATED PARK2 WILD-TYPE 
              9             107 
[1] "LARP4B MUTATION ANALYSIS"
[1] 3
  LARP4B MUTATED LARP4B WILD-TYPE 
               5              111 
  LARP4B MUTATED LARP4B WILD-TYPE 
               5              111 
[1] "OR6K3 MUTATION ANALYSIS"
[1] 3
  OR6K3 MUTATED OR6K3 WILD-TYPE 
              6             110 
  OR6K3 MUTATED OR6K3 WILD-TYPE 
              6             110 
[1] "TM7SF4 MUTATION ANALYSIS"
[1] 3
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               7              109 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               7              109 
[1] "UPF3A MUTATION ANALYSIS"
[1] 3
  UPF3A MUTATED UPF3A WILD-TYPE 
              6             110 
  UPF3A MUTATED UPF3A WILD-TYPE 
              6             110 
[1] "C7ORF63 MUTATION ANALYSIS"
[1] 3
  C7ORF63 MUTATED C7ORF63 WILD-TYPE 
                5               111 
  C7ORF63 MUTATED C7ORF63 WILD-TYPE 
                5               111 
[1] "KDM4B MUTATION ANALYSIS"
[1] 3
  KDM4B MUTATED KDM4B WILD-TYPE 
             10             106 
  KDM4B MUTATED KDM4B WILD-TYPE 
             10             106 
[1] "KIAA0748 MUTATION ANALYSIS"
[1] 3
  KIAA0748 MUTATED KIAA0748 WILD-TYPE 
                 7                109 
  KIAA0748 MUTATED KIAA0748 WILD-TYPE 
                 7                109 
[1] "OR8B4 MUTATION ANALYSIS"
[1] 3
  OR8B4 MUTATED OR8B4 WILD-TYPE 
              3             113 
  OR8B4 MUTATED OR8B4 WILD-TYPE 
              3             113 
[1] "POM121L12 MUTATION ANALYSIS"
[1] 3
  POM121L12 MUTATED POM121L12 WILD-TYPE 
                  7                 109 
  POM121L12 MUTATED POM121L12 WILD-TYPE 
                  7                 109 
[1] "RASA1 MUTATION ANALYSIS"
[1] 3
  RASA1 MUTATED RASA1 WILD-TYPE 
              9             107 
  RASA1 MUTATED RASA1 WILD-TYPE 
              9             107 
[1] "SLITRK6 MUTATION ANALYSIS"
[1] 3
  SLITRK6 MUTATED SLITRK6 WILD-TYPE 
               10               106 
  SLITRK6 MUTATED SLITRK6 WILD-TYPE 
               10               106 
[1] "TP53TG5 MUTATION ANALYSIS"
[1] 3
  TP53TG5 MUTATED TP53TG5 WILD-TYPE 
                4               112 
  TP53TG5 MUTATED TP53TG5 WILD-TYPE 
                4               112 
[1] "LHCGR MUTATION ANALYSIS"
[1] 3
  LHCGR MUTATED LHCGR WILD-TYPE 
              7             109 
  LHCGR MUTATED LHCGR WILD-TYPE 
              7             109 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 6 rows and 116 columns.

Variable 1:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 116 columns, 0 survival variables, and 6 non-survival variables.
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CBWD1 MUTATION ANALYSIS
D1V1, multiclass
        clus
vv       CBWD1 MUTATED CBWD1 WILD-TYPE
  CLUS_1             9              38
  CLUS_2             2              13
  CLUS_3             2               8
  CLUS_4             1              42
D1V2, multiclass
        clus
vv       CBWD1 MUTATED CBWD1 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             3              11
  CLUS_3             1              21
  CLUS_4             0              23
D1V3, multiclass
D1V4, multiclass
        clus
vv       CBWD1 MUTATED CBWD1 WILD-TYPE
  CLUS_1             2              30
  CLUS_2            10              37
  CLUS_3             2              23
D1V5, multiclass
        clus
vv       CBWD1 MUTATED CBWD1 WILD-TYPE
  CLUS_1            13              64
  CLUS_2             0              25
  CLUS_3             1              13
D1V6, multiclass
        clus
vv       CBWD1 MUTATED CBWD1 WILD-TYPE
  CLUS_1             1              25
  CLUS_2             2              21
  CLUS_3            11              56

Clustering(2) Variable = KRAS MUTATION ANALYSIS
D2V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           10             37
  CLUS_2            1             14
  CLUS_3            1              9
  CLUS_4            2             41
D2V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0              9
  CLUS_2            0             14
  CLUS_3            4             18
  CLUS_4            2             21
D2V3, multiclass
D2V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            5             27
  CLUS_2            7             40
  CLUS_3            0             25
D2V5, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           11             66
  CLUS_2            2             23
  CLUS_3            1             13
D2V6, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            2             24
  CLUS_2            4             19
  CLUS_3            8             59

Clustering(3) Variable = PGM5 MUTATION ANALYSIS
D3V1, multiclass
        clus
vv       PGM5 MUTATED PGM5 WILD-TYPE
  CLUS_1            9             38
  CLUS_2            3             12
  CLUS_3            3              7
  CLUS_4            1             42
D3V2, multiclass
        clus
vv       PGM5 MUTATED PGM5 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            5              9
  CLUS_3            1             21
  CLUS_4            0             23
D3V3, multiclass
D3V4, multiclass
        clus
vv       PGM5 MUTATED PGM5 WILD-TYPE
  CLUS_1            5             27
  CLUS_2            8             39
  CLUS_3            1             24
D3V5, multiclass
        clus
vv       PGM5 MUTATED PGM5 WILD-TYPE
  CLUS_1           14             63
  CLUS_2            1             24
  CLUS_3            1             13
D3V6, multiclass
        clus
vv       PGM5 MUTATED PGM5 WILD-TYPE
  CLUS_1            1             25
  CLUS_2            3             20
  CLUS_3           12             55

Clustering(4) Variable = RPL22 MUTATION ANALYSIS
D4V1, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             6              41
  CLUS_2             1              14
  CLUS_3             1               9
  CLUS_4             1              42
D4V2, multiclass
[1] "Remove cluster labels:" "RPL22 MUTATED"         
clus
  RPL22 MUTATED RPL22 WILD-TYPE 
              2              66 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-6452      TCGA-BR-6453 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-BR-6454      TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-BR-6458      TCGA-BR-6564      TCGA-BR-6565      TCGA-BR-6566 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-BR-6705      TCGA-BR-6706      TCGA-BR-6707      TCGA-BR-6709 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-BR-6710      TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-BR-6852      TCGA-CD-5798      TCGA-CD-5799      TCGA-CD-5800 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-CD-5801      TCGA-CD-5802      TCGA-CD-5803      TCGA-CD-5813 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-CG-4437      TCGA-CG-4441      TCGA-CG-5716      TCGA-CG-5717 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-CG-5718      TCGA-CG-5719      TCGA-CG-5720      TCGA-CG-5721 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-CG-5722      TCGA-CG-5723      TCGA-CG-5724      TCGA-CG-5725 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-CG-5727      TCGA-CG-5728      TCGA-CG-5730      TCGA-CG-5732 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-CG-5733      TCGA-CG-5734      TCGA-D7-5577      TCGA-D7-5578 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-D7-5579      TCGA-D7-6518      TCGA-D7-6519      TCGA-D7-6520 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-D7-6521      TCGA-D7-6522      TCGA-D7-6524      TCGA-D7-6525 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6528      TCGA-D7-6815 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-EQ-5647      TCGA-F1-6874 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
D4V3, multiclass
D4V4, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             0              32
  CLUS_2             6              41
  CLUS_3             2              23
D4V5, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             8              69
  CLUS_2             0              25
  CLUS_3             1              13
D4V6, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             1              25
  CLUS_2             0              23
  CLUS_3             8              59

Clustering(5) Variable = TP53 MUTATION ANALYSIS
D5V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           11             36
  CLUS_2            9              6
  CLUS_3            3              7
  CLUS_4           28             15
D5V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              7
  CLUS_2            6              8
  CLUS_3            7             15
  CLUS_4           17              6
D5V3, multiclass
D5V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           10             22
  CLUS_2           22             25
  CLUS_3           15             10
D5V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           28             49
  CLUS_2           12             13
  CLUS_3           12              2
D5V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           22              4
  CLUS_2            6             17
  CLUS_3           24             43

Clustering(6) Variable = TRIM48 MUTATION ANALYSIS
D6V1, multiclass
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              6               41
  CLUS_2              1               14
  CLUS_3              3                7
  CLUS_4              0               43
D6V2, multiclass
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              2               12
  CLUS_3              1               21
  CLUS_4              0               23
D6V3, multiclass
D6V4, multiclass
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              0               32
  CLUS_2              5               42
  CLUS_3              2               23
D6V5, multiclass
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1             10               67
  CLUS_2              0               25
  CLUS_3              0               14
D6V6, multiclass
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              0               26
  CLUS_2              0               23
  CLUS_3             10               57

Clustering(7) Variable = XPOT MUTATION ANALYSIS
D7V1, multiclass
        clus
vv       XPOT MUTATED XPOT WILD-TYPE
  CLUS_1            5             42
  CLUS_2            0             15
  CLUS_3            1              9
  CLUS_4            0             43
D7V2, multiclass
[1] "Remove cluster labels:" "XPOT MUTATED"          
clus
  XPOT MUTATED XPOT WILD-TYPE 
             1             67 
    TCGA-B7-5816     TCGA-B7-5818     TCGA-BR-6452     TCGA-BR-6453 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
    TCGA-BR-6454     TCGA-BR-6455     TCGA-BR-6456     TCGA-BR-6457 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
    TCGA-BR-6458     TCGA-BR-6564     TCGA-BR-6565     TCGA-BR-6566 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
    TCGA-BR-6705     TCGA-BR-6706     TCGA-BR-6707     TCGA-BR-6709 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
    TCGA-BR-6710     TCGA-BR-6801     TCGA-BR-6803     TCGA-BR-6852 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
    TCGA-CD-5798     TCGA-CD-5799     TCGA-CD-5800     TCGA-CD-5801 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
    TCGA-CD-5802     TCGA-CD-5803     TCGA-CD-5813     TCGA-CG-4437 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
    TCGA-CG-4441     TCGA-CG-5716     TCGA-CG-5717     TCGA-CG-5718 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
    TCGA-CG-5719     TCGA-CG-5720     TCGA-CG-5721     TCGA-CG-5722 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
    TCGA-CG-5723     TCGA-CG-5724     TCGA-CG-5725     TCGA-CG-5726 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
    TCGA-CG-5727     TCGA-CG-5728     TCGA-CG-5730     TCGA-CG-5732 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
    TCGA-CG-5733     TCGA-CG-5734     TCGA-D7-5577     TCGA-D7-5578 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
    TCGA-D7-5579     TCGA-D7-6518     TCGA-D7-6519     TCGA-D7-6520 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
    TCGA-D7-6521     TCGA-D7-6522     TCGA-D7-6524     TCGA-D7-6525 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
    TCGA-D7-6526     TCGA-D7-6527     TCGA-D7-6528     TCGA-D7-6815 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
    TCGA-D7-6817     TCGA-D7-6818     TCGA-D7-6820     TCGA-D7-6822 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
    TCGA-EQ-5647     TCGA-F1-6177     TCGA-F1-6874 
"XPOT WILD-TYPE" "XPOT WILD-TYPE" "XPOT WILD-TYPE" 
D7V3, multiclass
D7V4, multiclass
        clus
vv       XPOT MUTATED XPOT WILD-TYPE
  CLUS_1            1             31
  CLUS_2            4             43
  CLUS_3            0             25
D7V5, multiclass
        clus
vv       XPOT MUTATED XPOT WILD-TYPE
  CLUS_1            6             71
  CLUS_2            0             25
  CLUS_3            0             14
D7V6, multiclass
        clus
vv       XPOT MUTATED XPOT WILD-TYPE
  CLUS_1            0             26
  CLUS_2            0             23
  CLUS_3            6             61

Clustering(8) Variable = PIK3CA MUTATION ANALYSIS
D8V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             13               34
  CLUS_2              5               10
  CLUS_3              4                6
  CLUS_4              2               41
D8V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              9                0
  CLUS_2              4               10
  CLUS_3              3               19
  CLUS_4              2               21
D8V3, multiclass
D8V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              8               24
  CLUS_2             12               35
  CLUS_3              2               23
D8V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             21               56
  CLUS_2              1               24
  CLUS_3              2               12
D8V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2               24
  CLUS_2              2               21
  CLUS_3             20               47

Clustering(9) Variable = ACVR2A MUTATION ANALYSIS
D9V1, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1             11               36
  CLUS_2              1               14
  CLUS_3              1                9
  CLUS_4              0               43
D9V2, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              1                8
  CLUS_2              4               10
  CLUS_3              1               21
  CLUS_4              0               23
D9V3, multiclass
D9V4, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              2               30
  CLUS_2             10               37
  CLUS_3              1               24
D9V5, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1             13               64
  CLUS_2              0               25
  CLUS_3              0               14
D9V6, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              0               26
  CLUS_2              1               22
  CLUS_3             12               55

Clustering(10) Variable = RHOA MUTATION ANALYSIS
D10V1, multiclass
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  CLUS_1            5             42
  CLUS_2            1             14
  CLUS_3            0             10
  CLUS_4            1             42
D10V2, multiclass
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  CLUS_1            0              9
  CLUS_2            1             13
  CLUS_3            3             19
  CLUS_4            1             22
D10V3, multiclass
D10V4, multiclass
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  CLUS_1            2             30
  CLUS_2            3             44
  CLUS_3            1             24
D10V5, multiclass
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  CLUS_1            3             74
  CLUS_2            4             21
  CLUS_3            0             14
D10V6, multiclass
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  CLUS_1            1             25
  CLUS_2            1             22
  CLUS_3            5             62

Clustering(11) Variable = ARID1A MUTATION ANALYSIS
D11V1, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             15               32
  CLUS_2              2               13
  CLUS_3              5                5
  CLUS_4              0               43
D11V2, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              4                5
  CLUS_2              2               12
  CLUS_3              4               18
  CLUS_4              0               23
D11V3, multiclass
D11V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              9               23
  CLUS_2              9               38
  CLUS_3              2               23
D11V5, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             20               57
  CLUS_2              2               23
  CLUS_3              0               14
D11V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0               26
  CLUS_2              2               21
  CLUS_3             20               47

Clustering(12) Variable = OR8H3 MUTATION ANALYSIS
D12V1, multiclass
        clus
vv       OR8H3 MUTATED OR8H3 WILD-TYPE
  CLUS_1             2              45
  CLUS_2             4              11
  CLUS_3             2               8
  CLUS_4             2              41
D12V2, multiclass
        clus
vv       OR8H3 MUTATED OR8H3 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             4              10
  CLUS_3             1              21
  CLUS_4             1              22
D12V3, multiclass
D12V4, multiclass
        clus
vv       OR8H3 MUTATED OR8H3 WILD-TYPE
  CLUS_1             1              31
  CLUS_2             5              42
  CLUS_3             2              23
D12V5, multiclass
        clus
vv       OR8H3 MUTATED OR8H3 WILD-TYPE
  CLUS_1             9              68
  CLUS_2             0              25
  CLUS_3             1              13
D12V6, multiclass
        clus
vv       OR8H3 MUTATED OR8H3 WILD-TYPE
  CLUS_1             1              25
  CLUS_2             1              22
  CLUS_3             8              59

Clustering(13) Variable = EDNRB MUTATION ANALYSIS
D13V1, multiclass
        clus
vv       EDNRB MUTATED EDNRB WILD-TYPE
  CLUS_1             4              43
  CLUS_2             0              15
  CLUS_3             3               7
  CLUS_4             5              38
D13V2, multiclass
        clus
vv       EDNRB MUTATED EDNRB WILD-TYPE
  CLUS_1             0               9
  CLUS_2             2              12
  CLUS_3             1              21
  CLUS_4             1              22
D13V3, multiclass
D13V4, multiclass
        clus
vv       EDNRB MUTATED EDNRB WILD-TYPE
  CLUS_1             1              31
  CLUS_2             6              41
  CLUS_3             3              22
D13V5, multiclass
        clus
vv       EDNRB MUTATED EDNRB WILD-TYPE
  CLUS_1             9              68
  CLUS_2             1              24
  CLUS_3             2              12
D13V6, multiclass
        clus
vv       EDNRB MUTATED EDNRB WILD-TYPE
  CLUS_1             2              24
  CLUS_2             1              22
  CLUS_3             9              58

Clustering(14) Variable = ZNF804B MUTATION ANALYSIS
D14V1, multiclass
        clus
vv       ZNF804B MUTATED ZNF804B WILD-TYPE
  CLUS_1               4                43
  CLUS_2               4                11
  CLUS_3               2                 8
  CLUS_4               8                35
D14V2, multiclass
        clus
vv       ZNF804B MUTATED ZNF804B WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               5                 9
  CLUS_3               3                19
  CLUS_4               1                22
D14V3, multiclass
D14V4, multiclass
        clus
vv       ZNF804B MUTATED ZNF804B WILD-TYPE
  CLUS_1               0                32
  CLUS_2              11                36
  CLUS_3               6                19
D14V5, multiclass
        clus
vv       ZNF804B MUTATED ZNF804B WILD-TYPE
  CLUS_1              14                63
  CLUS_2               0                25
  CLUS_3               4                10
D14V6, multiclass
        clus
vv       ZNF804B MUTATED ZNF804B WILD-TYPE
  CLUS_1               5                21
  CLUS_2               1                22
  CLUS_3              12                55

Clustering(15) Variable = IRF2 MUTATION ANALYSIS
D15V1, multiclass
        clus
vv       IRF2 MUTATED IRF2 WILD-TYPE
  CLUS_1            5             42
  CLUS_2            1             14
  CLUS_3            2              8
  CLUS_4            0             43
D15V2, multiclass
        clus
vv       IRF2 MUTATED IRF2 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            2             12
  CLUS_3            0             22
  CLUS_4            0             23
D15V3, multiclass
D15V4, multiclass
        clus
vv       IRF2 MUTATED IRF2 WILD-TYPE
  CLUS_1            2             30
  CLUS_2            4             43
  CLUS_3            1             24
D15V5, multiclass
        clus
vv       IRF2 MUTATED IRF2 WILD-TYPE
  CLUS_1            8             69
  CLUS_2            0             25
  CLUS_3            0             14
D15V6, multiclass
        clus
vv       IRF2 MUTATED IRF2 WILD-TYPE
  CLUS_1            0             26
  CLUS_2            2             21
  CLUS_3            6             61

Clustering(16) Variable = IAPP MUTATION ANALYSIS
D16V1, multiclass
        clus
vv       IAPP MUTATED IAPP WILD-TYPE
  CLUS_1            3             44
  CLUS_2            0             15
  CLUS_3            0             10
  CLUS_4            1             42
D16V2, multiclass
[1] "Remove cluster labels:" "IAPP MUTATED"          
clus
  IAPP MUTATED IAPP WILD-TYPE 
             1             67 
    TCGA-B7-5816     TCGA-B7-5818     TCGA-BR-6452     TCGA-BR-6453 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-BR-6454     TCGA-BR-6455     TCGA-BR-6456     TCGA-BR-6457 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-BR-6458     TCGA-BR-6564     TCGA-BR-6565     TCGA-BR-6566 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-BR-6705     TCGA-BR-6706     TCGA-BR-6707     TCGA-BR-6709 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-BR-6710     TCGA-BR-6801     TCGA-BR-6802     TCGA-BR-6803 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-BR-6852     TCGA-CD-5798     TCGA-CD-5799     TCGA-CD-5800 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-CD-5801     TCGA-CD-5802     TCGA-CD-5803     TCGA-CD-5813 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-CG-4437     TCGA-CG-4441     TCGA-CG-5716     TCGA-CG-5717 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-CG-5718     TCGA-CG-5719     TCGA-CG-5720     TCGA-CG-5721 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-CG-5722     TCGA-CG-5723     TCGA-CG-5724     TCGA-CG-5725 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-CG-5726     TCGA-CG-5727     TCGA-CG-5728     TCGA-CG-5730 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-CG-5732     TCGA-CG-5733     TCGA-CG-5734     TCGA-D7-5577 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-D7-5578     TCGA-D7-5579     TCGA-D7-6518     TCGA-D7-6519 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-D7-6520     TCGA-D7-6521     TCGA-D7-6524     TCGA-D7-6525 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-D7-6526     TCGA-D7-6527     TCGA-D7-6528     TCGA-D7-6815 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-D7-6817     TCGA-D7-6818     TCGA-D7-6820     TCGA-D7-6822 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-EQ-5647     TCGA-F1-6177     TCGA-F1-6874 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
D16V3, multiclass
D16V4, multiclass
        clus
vv       IAPP MUTATED IAPP WILD-TYPE
  CLUS_1            2             30
  CLUS_2            1             46
  CLUS_3            0             25
D16V5, multiclass
        clus
vv       IAPP MUTATED IAPP WILD-TYPE
  CLUS_1            1             76
  CLUS_2            2             23
  CLUS_3            1             13
D16V6, multiclass
        clus
vv       IAPP MUTATED IAPP WILD-TYPE
  CLUS_1            1             25
  CLUS_2            1             22
  CLUS_3            2             65

Clustering(17) Variable = PCDH15 MUTATION ANALYSIS
D17V1, multiclass
        clus
vv       PCDH15 MUTATED PCDH15 WILD-TYPE
  CLUS_1             11               36
  CLUS_2              3               12
  CLUS_3              1                9
  CLUS_4              6               37
D17V2, multiclass
        clus
vv       PCDH15 MUTATED PCDH15 WILD-TYPE
  CLUS_1              2                7
  CLUS_2              2               12
  CLUS_3              3               19
  CLUS_4              5               18
D17V3, multiclass
D17V4, multiclass
        clus
vv       PCDH15 MUTATED PCDH15 WILD-TYPE
  CLUS_1              8               24
  CLUS_2              8               39
  CLUS_3              3               22
D17V5, multiclass
        clus
vv       PCDH15 MUTATED PCDH15 WILD-TYPE
  CLUS_1             17               60
  CLUS_2              3               22
  CLUS_3              2               12
D17V6, multiclass
        clus
vv       PCDH15 MUTATED PCDH15 WILD-TYPE
  CLUS_1              5               21
  CLUS_2              5               18
  CLUS_3             12               55

Clustering(18) Variable = SPRYD5 MUTATION ANALYSIS
D18V1, multiclass
        clus
vv       SPRYD5 MUTATED SPRYD5 WILD-TYPE
  CLUS_1              4               43
  CLUS_2              1               14
  CLUS_3              1                9
  CLUS_4              2               41
D18V2, multiclass
        clus
vv       SPRYD5 MUTATED SPRYD5 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              3               11
  CLUS_3              1               21
  CLUS_4              0               23
D18V3, multiclass
D18V4, multiclass
        clus
vv       SPRYD5 MUTATED SPRYD5 WILD-TYPE
  CLUS_1              2               30
  CLUS_2              5               42
  CLUS_3              1               24
D18V5, multiclass
        clus
vv       SPRYD5 MUTATED SPRYD5 WILD-TYPE
  CLUS_1              7               70
  CLUS_2              0               25
  CLUS_3              1               13
D18V6, multiclass
        clus
vv       SPRYD5 MUTATED SPRYD5 WILD-TYPE
  CLUS_1              1               25
  CLUS_2              1               22
  CLUS_3              6               61

Clustering(19) Variable = TUSC3 MUTATION ANALYSIS
D19V1, multiclass
        clus
vv       TUSC3 MUTATED TUSC3 WILD-TYPE
  CLUS_1             5              42
  CLUS_2             1              14
  CLUS_3             1               9
  CLUS_4             2              41
D19V2, multiclass
        clus
vv       TUSC3 MUTATED TUSC3 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             1              13
  CLUS_3             3              19
  CLUS_4             2              21
D19V3, multiclass
D19V4, multiclass
        clus
vv       TUSC3 MUTATED TUSC3 WILD-TYPE
  CLUS_1             2              30
  CLUS_2             3              44
  CLUS_3             2              23
D19V5, multiclass
        clus
vv       TUSC3 MUTATED TUSC3 WILD-TYPE
  CLUS_1             6              71
  CLUS_2             2              23
  CLUS_3             1              13
D19V6, multiclass
        clus
vv       TUSC3 MUTATED TUSC3 WILD-TYPE
  CLUS_1             3              23
  CLUS_2             1              22
  CLUS_3             5              62

Clustering(20) Variable = FGF22 MUTATION ANALYSIS
D20V1, multiclass
        clus
vv       FGF22 MUTATED FGF22 WILD-TYPE
  CLUS_1             1              46
  CLUS_2             0              15
  CLUS_3             2               8
  CLUS_4             0              43
D20V2, multiclass
[1] "Remove cluster labels:" "FGF22 MUTATED"         
clus
  FGF22 MUTATED FGF22 WILD-TYPE 
              1              67 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-6453      TCGA-BR-6454 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-BR-6455      TCGA-BR-6456      TCGA-BR-6457      TCGA-BR-6458 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-BR-6564      TCGA-BR-6565      TCGA-BR-6566      TCGA-BR-6705 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-BR-6706      TCGA-BR-6707      TCGA-BR-6709      TCGA-BR-6710 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-BR-6801      TCGA-BR-6802      TCGA-BR-6803      TCGA-BR-6852 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-CD-5798      TCGA-CD-5799      TCGA-CD-5800      TCGA-CD-5801 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-CD-5802      TCGA-CD-5803      TCGA-CD-5813      TCGA-CG-4437 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-CG-4441      TCGA-CG-5716      TCGA-CG-5717      TCGA-CG-5718 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-CG-5719      TCGA-CG-5720      TCGA-CG-5721      TCGA-CG-5722 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-CG-5723      TCGA-CG-5724      TCGA-CG-5725      TCGA-CG-5726 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-CG-5727      TCGA-CG-5728      TCGA-CG-5730      TCGA-CG-5732 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-CG-5733      TCGA-CG-5734      TCGA-D7-5577      TCGA-D7-5578 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-D7-5579      TCGA-D7-6518      TCGA-D7-6519      TCGA-D7-6520 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-D7-6521      TCGA-D7-6522      TCGA-D7-6524      TCGA-D7-6525 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6528      TCGA-D7-6815 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-EQ-5647      TCGA-F1-6177      TCGA-F1-6874 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
D20V3, multiclass
D20V4, multiclass
        clus
vv       FGF22 MUTATED FGF22 WILD-TYPE
  CLUS_1             0              32
  CLUS_2             3              44
  CLUS_3             0              25
D20V5, multiclass
        clus
vv       FGF22 MUTATED FGF22 WILD-TYPE
  CLUS_1             3              74
  CLUS_2             0              25
  CLUS_3             0              14
D20V6, multiclass
        clus
vv       FGF22 MUTATED FGF22 WILD-TYPE
  CLUS_1             0              26
  CLUS_2             0              23
  CLUS_3             3              64

Clustering(21) Variable = HLA-B MUTATION ANALYSIS
D21V1, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             7              40
  CLUS_2             1              14
  CLUS_3             0              10
  CLUS_4             1              42
D21V2, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             2               7
  CLUS_2             3              11
  CLUS_3             0              22
  CLUS_4             0              23
D21V3, multiclass
D21V4, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             0              32
  CLUS_2             5              42
  CLUS_3             3              22
D21V5, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             8              69
  CLUS_2             0              25
  CLUS_3             1              13
D21V6, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             1              25
  CLUS_2             1              22
  CLUS_3             7              60

Clustering(22) Variable = PTH2 MUTATION ANALYSIS
D22V1, multiclass
        clus
vv       PTH2 MUTATED PTH2 WILD-TYPE
  CLUS_1            1             46
  CLUS_2            0             15
  CLUS_3            0             10
  CLUS_4            2             41
D22V2, multiclass
        clus
vv       PTH2 MUTATED PTH2 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            0             14
  CLUS_3            0             22
  CLUS_4            2             21
D22V3, multiclass
D22V4, multiclass
        clus
vv       PTH2 MUTATED PTH2 WILD-TYPE
  CLUS_1            2             30
  CLUS_2            0             47
  CLUS_3            1             24
D22V5, multiclass
        clus
vv       PTH2 MUTATED PTH2 WILD-TYPE
  CLUS_1            1             76
  CLUS_2            2             23
  CLUS_3            0             14
D22V6, multiclass
        clus
vv       PTH2 MUTATED PTH2 WILD-TYPE
  CLUS_1            1             25
  CLUS_2            1             22
  CLUS_3            1             66

Clustering(23) Variable = C17ORF63 MUTATION ANALYSIS
D23V1, multiclass
        clus
vv       C17ORF63 MUTATED C17ORF63 WILD-TYPE
  CLUS_1                2                 45
  CLUS_2                1                 14
  CLUS_3                0                 10
  CLUS_4                0                 43
D23V2, multiclass
[1] "Remove cluster labels:" "C17ORF63 MUTATED"      
clus
  C17ORF63 MUTATED C17ORF63 WILD-TYPE 
                 1                 67 
        TCGA-B7-5818         TCGA-BR-6452         TCGA-BR-6453 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-BR-6454         TCGA-BR-6455         TCGA-BR-6456 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-BR-6457         TCGA-BR-6458         TCGA-BR-6564 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-BR-6565         TCGA-BR-6566         TCGA-BR-6705 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-BR-6706         TCGA-BR-6707         TCGA-BR-6709 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-BR-6710         TCGA-BR-6801         TCGA-BR-6802 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-BR-6803         TCGA-BR-6852         TCGA-CD-5798 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CD-5813 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4441         TCGA-CG-5716 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-F1-6177 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-F1-6874 
"C17ORF63 WILD-TYPE" 
D23V3, multiclass
D23V4, multiclass
        clus
vv       C17ORF63 MUTATED C17ORF63 WILD-TYPE
  CLUS_1                1                 31
  CLUS_2                1                 46
  CLUS_3                1                 24
D23V5, multiclass
        clus
vv       C17ORF63 MUTATED C17ORF63 WILD-TYPE
  CLUS_1                3                 74
  CLUS_2                0                 25
  CLUS_3                0                 14
D23V6, multiclass
        clus
vv       C17ORF63 MUTATED C17ORF63 WILD-TYPE
  CLUS_1                0                 26
  CLUS_2                1                 22
  CLUS_3                2                 65

Clustering(24) Variable = SMAD4 MUTATION ANALYSIS
D24V1, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             3              44
  CLUS_2             1              14
  CLUS_3             0              10
  CLUS_4             3              40
D24V2, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             0              14
  CLUS_3             1              21
  CLUS_4             2              21
D24V3, multiclass
D24V4, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             2              30
  CLUS_2             4              43
  CLUS_3             0              25
D24V5, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             5              72
  CLUS_2             1              24
  CLUS_3             1              13
D24V6, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             1              25
  CLUS_2             2              21
  CLUS_3             4              63

Clustering(25) Variable = POTEG MUTATION ANALYSIS
D25V1, multiclass
        clus
vv       POTEG MUTATED POTEG WILD-TYPE
  CLUS_1             5              42
  CLUS_2             0              15
  CLUS_3             0              10
  CLUS_4             1              42
D25V2, multiclass
        clus
vv       POTEG MUTATED POTEG WILD-TYPE
  CLUS_1             0               9
  CLUS_2             1              13
  CLUS_3             2              20
  CLUS_4             0              23
D25V3, multiclass
D25V4, multiclass
        clus
vv       POTEG MUTATED POTEG WILD-TYPE
  CLUS_1             1              31
  CLUS_2             3              44
  CLUS_3             1              24
D25V5, multiclass
        clus
vv       POTEG MUTATED POTEG WILD-TYPE
  CLUS_1             5              72
  CLUS_2             1              24
  CLUS_3             0              14
D25V6, multiclass
        clus
vv       POTEG MUTATED POTEG WILD-TYPE
  CLUS_1             0              26
  CLUS_2             2              21
  CLUS_3             4              63

Clustering(26) Variable = RNF43 MUTATION ANALYSIS
D26V1, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             9              38
  CLUS_2             2              13
  CLUS_3             2               8
  CLUS_4             0              43
D26V2, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             4              10
  CLUS_3             2              20
  CLUS_4             0              23
D26V3, multiclass
D26V4, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             3              29
  CLUS_2             8              39
  CLUS_3             0              25
D26V5, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1            13              64
  CLUS_2             0              25
  CLUS_3             0              14
D26V6, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             0              26
  CLUS_2             2              21
  CLUS_3            11              56

Clustering(27) Variable = WBSCR17 MUTATION ANALYSIS
D27V1, multiclass
        clus
vv       WBSCR17 MUTATED WBSCR17 WILD-TYPE
  CLUS_1               6                41
  CLUS_2               2                13
  CLUS_3               2                 8
  CLUS_4               2                41
D27V2, multiclass
        clus
vv       WBSCR17 MUTATED WBSCR17 WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               5                 9
  CLUS_3               2                20
  CLUS_4               0                23
D27V3, multiclass
D27V4, multiclass
        clus
vv       WBSCR17 MUTATED WBSCR17 WILD-TYPE
  CLUS_1               2                30
  CLUS_2               5                42
  CLUS_3               2                23
D27V5, multiclass
        clus
vv       WBSCR17 MUTATED WBSCR17 WILD-TYPE
  CLUS_1              12                65
  CLUS_2               0                25
  CLUS_3               0                14
D27V6, multiclass
        clus
vv       WBSCR17 MUTATED WBSCR17 WILD-TYPE
  CLUS_1               1                25
  CLUS_2               2                21
  CLUS_3               9                58

Clustering(28) Variable = PHF2 MUTATION ANALYSIS
D28V1, multiclass
        clus
vv       PHF2 MUTATED PHF2 WILD-TYPE
  CLUS_1            9             38
  CLUS_2            1             14
  CLUS_3            2              8
  CLUS_4            0             43
D28V2, multiclass
        clus
vv       PHF2 MUTATED PHF2 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            4             10
  CLUS_3            1             21
  CLUS_4            0             23
D28V3, multiclass
D28V4, multiclass
        clus
vv       PHF2 MUTATED PHF2 WILD-TYPE
  CLUS_1            0             32
  CLUS_2            8             39
  CLUS_3            2             23
D28V5, multiclass
        clus
vv       PHF2 MUTATED PHF2 WILD-TYPE
  CLUS_1           12             65
  CLUS_2            0             25
  CLUS_3            0             14
D28V6, multiclass
        clus
vv       PHF2 MUTATED PHF2 WILD-TYPE
  CLUS_1            0             26
  CLUS_2            0             23
  CLUS_3           12             55

Clustering(29) Variable = TPTE MUTATION ANALYSIS
D29V1, multiclass
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1            8             39
  CLUS_2            1             14
  CLUS_3            0             10
  CLUS_4            5             38
D29V2, multiclass
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1            1              8
  CLUS_2            1             13
  CLUS_3            2             20
  CLUS_4            3             20
D29V3, multiclass
D29V4, multiclass
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1            3             29
  CLUS_2            6             41
  CLUS_3            4             21
D29V5, multiclass
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1           11             66
  CLUS_2            0             25
  CLUS_3            3             11
D29V6, multiclass
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1            4             22
  CLUS_2            2             21
  CLUS_3            8             59

Clustering(30) Variable = CDH1 MUTATION ANALYSIS
D30V1, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            6             41
  CLUS_2            1             14
  CLUS_3            2              8
  CLUS_4            1             42
D30V2, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            2             12
  CLUS_3            3             19
  CLUS_4            2             21
D30V3, multiclass
D30V4, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            5             27
  CLUS_2            5             42
  CLUS_3            0             25
D30V5, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            6             71
  CLUS_2            5             20
  CLUS_3            0             14
D30V6, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            0             26
  CLUS_2            4             19
  CLUS_3            7             60

Clustering(31) Variable = CPS1 MUTATION ANALYSIS
D31V1, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            6             41
  CLUS_2            1             14
  CLUS_3            2              8
  CLUS_4            4             39
D31V2, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            2             12
  CLUS_3            2             20
  CLUS_4            0             23
D31V3, multiclass
D31V4, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            4             28
  CLUS_2            6             41
  CLUS_3            2             23
D31V5, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1           10             67
  CLUS_2            2             23
  CLUS_3            1             13
D31V6, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            1             25
  CLUS_2            2             21
  CLUS_3           10             57

Clustering(32) Variable = INO80E MUTATION ANALYSIS
D32V1, multiclass
        clus
vv       INO80E MUTATED INO80E WILD-TYPE
  CLUS_1              4               43
  CLUS_2              0               15
  CLUS_3              0               10
  CLUS_4              1               42
D32V2, multiclass
[1] "Remove cluster labels:" "INO80E MUTATED"        
clus
  INO80E MUTATED INO80E WILD-TYPE 
               1               67 
      TCGA-B7-5816       TCGA-B7-5818       TCGA-BR-6452       TCGA-BR-6453 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
      TCGA-BR-6454       TCGA-BR-6455       TCGA-BR-6456       TCGA-BR-6457 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
      TCGA-BR-6458       TCGA-BR-6564       TCGA-BR-6565       TCGA-BR-6566 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
      TCGA-BR-6705       TCGA-BR-6706       TCGA-BR-6707       TCGA-BR-6709 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
      TCGA-BR-6710       TCGA-BR-6801       TCGA-BR-6802       TCGA-BR-6803 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
      TCGA-BR-6852       TCGA-CD-5798       TCGA-CD-5799       TCGA-CD-5800 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
      TCGA-CD-5801       TCGA-CD-5802       TCGA-CD-5803       TCGA-CD-5813 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
      TCGA-CG-4437       TCGA-CG-4441       TCGA-CG-5716       TCGA-CG-5717 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
      TCGA-CG-5718       TCGA-CG-5719       TCGA-CG-5720       TCGA-CG-5722 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
      TCGA-CG-5723       TCGA-CG-5724       TCGA-CG-5725       TCGA-CG-5726 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
      TCGA-CG-5727       TCGA-CG-5728       TCGA-CG-5730       TCGA-CG-5732 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
      TCGA-CG-5733       TCGA-CG-5734       TCGA-D7-5577       TCGA-D7-5578 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
      TCGA-D7-5579       TCGA-D7-6518       TCGA-D7-6519       TCGA-D7-6520 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
      TCGA-D7-6521       TCGA-D7-6522       TCGA-D7-6524       TCGA-D7-6525 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
      TCGA-D7-6526       TCGA-D7-6527       TCGA-D7-6528       TCGA-D7-6815 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
      TCGA-D7-6817       TCGA-D7-6818       TCGA-D7-6820       TCGA-D7-6822 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
      TCGA-EQ-5647       TCGA-F1-6177       TCGA-F1-6874 
"INO80E WILD-TYPE" "INO80E WILD-TYPE" "INO80E WILD-TYPE" 
D32V3, multiclass
D32V4, multiclass
        clus
vv       INO80E MUTATED INO80E WILD-TYPE
  CLUS_1              1               31
  CLUS_2              2               45
  CLUS_3              2               23
D32V5, multiclass
        clus
vv       INO80E MUTATED INO80E WILD-TYPE
  CLUS_1              4               73
  CLUS_2              0               25
  CLUS_3              1               13
D32V6, multiclass
        clus
vv       INO80E MUTATED INO80E WILD-TYPE
  CLUS_1              1               25
  CLUS_2              1               22
  CLUS_3              3               64

Clustering(33) Variable = ELF3 MUTATION ANALYSIS
D33V1, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            4             43
  CLUS_2            0             15
  CLUS_3            1              9
  CLUS_4            0             43
D33V2, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            2             12
  CLUS_3            1             21
  CLUS_4            0             23
D33V3, multiclass
D33V4, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            0             32
  CLUS_2            3             44
  CLUS_3            1             24
D33V5, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            5             72
  CLUS_2            0             25
  CLUS_3            0             14
D33V6, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            0             26
  CLUS_2            0             23
  CLUS_3            5             62

Clustering(34) Variable = PARK2 MUTATION ANALYSIS
D34V1, multiclass
        clus
vv       PARK2 MUTATED PARK2 WILD-TYPE
  CLUS_1             3              44
  CLUS_2             2              13
  CLUS_3             2               8
  CLUS_4             2              41
D34V2, multiclass
        clus
vv       PARK2 MUTATED PARK2 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             3              11
  CLUS_3             0              22
  CLUS_4             1              22
D34V3, multiclass
D34V4, multiclass
        clus
vv       PARK2 MUTATED PARK2 WILD-TYPE
  CLUS_1             1              31
  CLUS_2             8              39
  CLUS_3             0              25
D34V5, multiclass
        clus
vv       PARK2 MUTATED PARK2 WILD-TYPE
  CLUS_1             7              70
  CLUS_2             1              24
  CLUS_3             1              13
D34V6, multiclass
        clus
vv       PARK2 MUTATED PARK2 WILD-TYPE
  CLUS_1             1              25
  CLUS_2             1              22
  CLUS_3             7              60

Clustering(35) Variable = LARP4B MUTATION ANALYSIS
D35V1, multiclass
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  CLUS_1              3               44
  CLUS_2              0               15
  CLUS_3              2                8
  CLUS_4              0               43
D35V2, multiclass
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  CLUS_1              0                9
  CLUS_2              2               12
  CLUS_3              1               21
  CLUS_4              0               23
D35V3, multiclass
D35V4, multiclass
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  CLUS_1              0               32
  CLUS_2              3               44
  CLUS_3              1               24
D35V5, multiclass
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  CLUS_1              5               72
  CLUS_2              0               25
  CLUS_3              0               14
D35V6, multiclass
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  CLUS_1              0               26
  CLUS_2              0               23
  CLUS_3              5               62

Clustering(36) Variable = OR6K3 MUTATION ANALYSIS
D36V1, multiclass
        clus
vv       OR6K3 MUTATED OR6K3 WILD-TYPE
  CLUS_1             4              43
  CLUS_2             0              15
  CLUS_3             1               9
  CLUS_4             1              42
D36V2, multiclass
        clus
vv       OR6K3 MUTATED OR6K3 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             1              13
  CLUS_3             1              21
  CLUS_4             0              23
D36V3, multiclass
D36V4, multiclass
        clus
vv       OR6K3 MUTATED OR6K3 WILD-TYPE
  CLUS_1             2              30
  CLUS_2             2              45
  CLUS_3             2              23
D36V5, multiclass
        clus
vv       OR6K3 MUTATED OR6K3 WILD-TYPE
  CLUS_1             5              72
  CLUS_2             0              25
  CLUS_3             1              13
D36V6, multiclass
        clus
vv       OR6K3 MUTATED OR6K3 WILD-TYPE
  CLUS_1             1              25
  CLUS_2             1              22
  CLUS_3             4              63

Clustering(37) Variable = TM7SF4 MUTATION ANALYSIS
D37V1, multiclass
        clus
vv       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  CLUS_1              4               43
  CLUS_2              1               14
  CLUS_3              0               10
  CLUS_4              2               41
D37V2, multiclass
        clus
vv       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              2               12
  CLUS_3              2               20
  CLUS_4              0               23
D37V3, multiclass
D37V4, multiclass
        clus
vv       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  CLUS_1              3               29
  CLUS_2              3               44
  CLUS_3              1               24
D37V5, multiclass
        clus
vv       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  CLUS_1              6               71
  CLUS_2              1               24
  CLUS_3              0               14
D37V6, multiclass
        clus
vv       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  CLUS_1              0               26
  CLUS_2              2               21
  CLUS_3              5               62

Clustering(38) Variable = UPF3A MUTATION ANALYSIS
D38V1, multiclass
        clus
vv       UPF3A MUTATED UPF3A WILD-TYPE
  CLUS_1             4              43
  CLUS_2             0              15
  CLUS_3             1               9
  CLUS_4             1              42
D38V2, multiclass
        clus
vv       UPF3A MUTATED UPF3A WILD-TYPE
  CLUS_1             0               9
  CLUS_2             2              12
  CLUS_3             1              21
  CLUS_4             0              23
D38V3, multiclass
D38V4, multiclass
        clus
vv       UPF3A MUTATED UPF3A WILD-TYPE
  CLUS_1             0              32
  CLUS_2             4              43
  CLUS_3             2              23
D38V5, multiclass
        clus
vv       UPF3A MUTATED UPF3A WILD-TYPE
  CLUS_1             5              72
  CLUS_2             0              25
  CLUS_3             1              13
D38V6, multiclass
        clus
vv       UPF3A MUTATED UPF3A WILD-TYPE
  CLUS_1             1              25
  CLUS_2             0              23
  CLUS_3             5              62

Clustering(39) Variable = C7ORF63 MUTATION ANALYSIS
D39V1, multiclass
        clus
vv       C7ORF63 MUTATED C7ORF63 WILD-TYPE
  CLUS_1               4                43
  CLUS_2               0                15
  CLUS_3               1                 9
  CLUS_4               0                43
D39V2, multiclass
D39V3, multiclass
D39V4, multiclass
        clus
vv       C7ORF63 MUTATED C7ORF63 WILD-TYPE
  CLUS_1               1                31
  CLUS_2               3                44
  CLUS_3               0                25
D39V5, multiclass
        clus
vv       C7ORF63 MUTATED C7ORF63 WILD-TYPE
  CLUS_1               5                72
  CLUS_2               0                25
  CLUS_3               0                14
D39V6, multiclass
        clus
vv       C7ORF63 MUTATED C7ORF63 WILD-TYPE
  CLUS_1               0                26
  CLUS_2               1                22
  CLUS_3               4                63

Clustering(40) Variable = KDM4B MUTATION ANALYSIS
D40V1, multiclass
        clus
vv       KDM4B MUTATED KDM4B WILD-TYPE
  CLUS_1             6              41
  CLUS_2             0              15
  CLUS_3             3               7
  CLUS_4             1              42
D40V2, multiclass
        clus
vv       KDM4B MUTATED KDM4B WILD-TYPE
  CLUS_1             0               9
  CLUS_2             3              11
  CLUS_3             1              21
  CLUS_4             0              23
D40V3, multiclass
D40V4, multiclass
        clus
vv       KDM4B MUTATED KDM4B WILD-TYPE
  CLUS_1             3              29
  CLUS_2             2              45
  CLUS_3             2              23
D40V5, multiclass
        clus
vv       KDM4B MUTATED KDM4B WILD-TYPE
  CLUS_1             9              68
  CLUS_2             0              25
  CLUS_3             1              13
D40V6, multiclass
        clus
vv       KDM4B MUTATED KDM4B WILD-TYPE
  CLUS_1             1              25
  CLUS_2             3              20
  CLUS_3             6              61

Clustering(41) Variable = KIAA0748 MUTATION ANALYSIS
D41V1, multiclass
        clus
vv       KIAA0748 MUTATED KIAA0748 WILD-TYPE
  CLUS_1                3                 44
  CLUS_2                0                 15
  CLUS_3                0                 10
  CLUS_4                4                 39
D41V2, multiclass
        clus
vv       KIAA0748 MUTATED KIAA0748 WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                2                 12
  CLUS_3                1                 21
  CLUS_4                1                 22
D41V3, multiclass
D41V4, multiclass
        clus
vv       KIAA0748 MUTATED KIAA0748 WILD-TYPE
  CLUS_1                1                 31
  CLUS_2                5                 42
  CLUS_3                1                 24
D41V5, multiclass
        clus
vv       KIAA0748 MUTATED KIAA0748 WILD-TYPE
  CLUS_1                6                 71
  CLUS_2                1                 24
  CLUS_3                0                 14
D41V6, multiclass
        clus
vv       KIAA0748 MUTATED KIAA0748 WILD-TYPE
  CLUS_1                1                 25
  CLUS_2                0                 23
  CLUS_3                6                 61

Clustering(42) Variable = OR8B4 MUTATION ANALYSIS
D42V1, multiclass
        clus
vv       OR8B4 MUTATED OR8B4 WILD-TYPE
  CLUS_1             0              47
  CLUS_2             0              15
  CLUS_3             1               9
  CLUS_4             2              41
D42V2, multiclass
        clus
vv       OR8B4 MUTATED OR8B4 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             3              11
  CLUS_3             0              22
  CLUS_4             0              23
D42V3, multiclass
[1] "Remove cluster labels:" "OR8B4 MUTATED"         
clus
  OR8B4 MUTATED OR8B4 WILD-TYPE 
              2             102 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-4187      TCGA-BR-4191 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-4201      TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-4257      TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-4292      TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-4362      TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4367 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-4368      TCGA-BR-4369      TCGA-BR-4370      TCGA-BR-4371 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-6452      TCGA-BR-6453      TCGA-BR-6454      TCGA-BR-6455 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-6456      TCGA-BR-6457      TCGA-BR-6458      TCGA-BR-6564 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-6565      TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-6707      TCGA-BR-6709      TCGA-BR-6710      TCGA-BR-6801 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-6802      TCGA-BR-6803      TCGA-BR-6852      TCGA-CD-5798 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CD-5799      TCGA-CD-5800      TCGA-CD-5801      TCGA-CD-5803 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CD-5813      TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-4306      TCGA-CG-4436      TCGA-CG-4437      TCGA-CG-4438 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-4440      TCGA-CG-4441      TCGA-CG-4442      TCGA-CG-4443 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-4444      TCGA-CG-4449      TCGA-CG-4460      TCGA-CG-4462 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-4465      TCGA-CG-4466      TCGA-CG-4469      TCGA-CG-4472 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-4474      TCGA-CG-4475      TCGA-CG-4476      TCGA-CG-4477 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-5716      TCGA-CG-5717      TCGA-CG-5718      TCGA-CG-5719 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-5720      TCGA-CG-5721      TCGA-CG-5722      TCGA-CG-5723 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-5724      TCGA-CG-5725      TCGA-CG-5726      TCGA-CG-5732 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-5734      TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-6518 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-D7-6524      TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6815 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-F1-6177      TCGA-F1-6874 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
D42V4, multiclass
[1] "Remove cluster labels:" "OR8B4 MUTATED"         
clus
  OR8B4 MUTATED OR8B4 WILD-TYPE 
              2             102 
     TCGA-B7-5816      TCGA-B7-5818      TCGA-BR-4187      TCGA-BR-4191 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-4201      TCGA-BR-4253      TCGA-BR-4255      TCGA-BR-4256 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-4257      TCGA-BR-4267      TCGA-BR-4279      TCGA-BR-4280 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-4292      TCGA-BR-4294      TCGA-BR-4357      TCGA-BR-4361 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-4362      TCGA-BR-4363      TCGA-BR-4366      TCGA-BR-4367 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-4368      TCGA-BR-4369      TCGA-BR-4370      TCGA-BR-4371 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-6452      TCGA-BR-6453      TCGA-BR-6454      TCGA-BR-6455 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-6456      TCGA-BR-6457      TCGA-BR-6458      TCGA-BR-6564 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-6565      TCGA-BR-6566      TCGA-BR-6705      TCGA-BR-6706 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-6707      TCGA-BR-6709      TCGA-BR-6710      TCGA-BR-6801 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-BR-6802      TCGA-BR-6803      TCGA-BR-6852      TCGA-CD-5798 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CD-5799      TCGA-CD-5800      TCGA-CD-5801      TCGA-CD-5803 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CD-5813      TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-4306      TCGA-CG-4436      TCGA-CG-4437      TCGA-CG-4438 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-4440      TCGA-CG-4441      TCGA-CG-4442      TCGA-CG-4443 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-4444      TCGA-CG-4449      TCGA-CG-4460      TCGA-CG-4462 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-4465      TCGA-CG-4466      TCGA-CG-4469      TCGA-CG-4472 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-4474      TCGA-CG-4475      TCGA-CG-4476      TCGA-CG-4477 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-5716      TCGA-CG-5717      TCGA-CG-5718      TCGA-CG-5719 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-5720      TCGA-CG-5721      TCGA-CG-5722      TCGA-CG-5723 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-5724      TCGA-CG-5725      TCGA-CG-5726      TCGA-CG-5732 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-CG-5734      TCGA-D7-5577      TCGA-D7-5578      TCGA-D7-6518 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-D7-6519      TCGA-D7-6520      TCGA-D7-6521      TCGA-D7-6522 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-D7-6524      TCGA-D7-6526      TCGA-D7-6527      TCGA-D7-6815 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-D7-6817      TCGA-D7-6818      TCGA-D7-6820      TCGA-D7-6822 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
     TCGA-F1-6177      TCGA-F1-6874 
"OR8B4 WILD-TYPE" "OR8B4 WILD-TYPE" 
D42V5, multiclass
        clus
vv       OR8B4 MUTATED OR8B4 WILD-TYPE
  CLUS_1             3              74
  CLUS_2             0              25
  CLUS_3             0              14
D42V6, multiclass
        clus
vv       OR8B4 MUTATED OR8B4 WILD-TYPE
  CLUS_1             0              26
  CLUS_2             0              23
  CLUS_3             3              64

Clustering(43) Variable = POM121L12 MUTATION ANALYSIS
D43V1, multiclass
        clus
vv       POM121L12 MUTATED POM121L12 WILD-TYPE
  CLUS_1                 6                  41
  CLUS_2                 1                  14
  CLUS_3                 0                  10
  CLUS_4                 0                  43
D43V2, multiclass
        clus
vv       POM121L12 MUTATED POM121L12 WILD-TYPE
  CLUS_1                 1                   8
  CLUS_2                 0                  14
  CLUS_3                 3                  19
  CLUS_4                 0                  23
D43V3, multiclass
D43V4, multiclass
        clus
vv       POM121L12 MUTATED POM121L12 WILD-TYPE
  CLUS_1                 3                  29
  CLUS_2                 1                  46
  CLUS_3                 3                  22
D43V5, multiclass
        clus
vv       POM121L12 MUTATED POM121L12 WILD-TYPE
  CLUS_1                 6                  71
  CLUS_2                 1                  24
  CLUS_3                 0                  14
D43V6, multiclass
        clus
vv       POM121L12 MUTATED POM121L12 WILD-TYPE
  CLUS_1                 0                  26
  CLUS_2                 2                  21
  CLUS_3                 5                  62

Clustering(44) Variable = RASA1 MUTATION ANALYSIS
D44V1, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             2              45
  CLUS_2             2              13
  CLUS_3             1               9
  CLUS_4             4              39
D44V2, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             1              13
  CLUS_3             0              22
  CLUS_4             2              21
D44V3, multiclass
D44V4, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             0              32
  CLUS_2             8              39
  CLUS_3             1              24
D44V5, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             6              71
  CLUS_2             0              25
  CLUS_3             3              11
D44V6, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             3              23
  CLUS_2             0              23
  CLUS_3             6              61

Clustering(45) Variable = SLITRK6 MUTATION ANALYSIS
D45V1, multiclass
        clus
vv       SLITRK6 MUTATED SLITRK6 WILD-TYPE
  CLUS_1               4                43
  CLUS_2               3                12
  CLUS_3               1                 9
  CLUS_4               2                41
D45V2, multiclass
        clus
vv       SLITRK6 MUTATED SLITRK6 WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               1                13
  CLUS_3               3                19
  CLUS_4               2                21
D45V3, multiclass
D45V4, multiclass
        clus
vv       SLITRK6 MUTATED SLITRK6 WILD-TYPE
  CLUS_1               2                30
  CLUS_2               5                42
  CLUS_3               1                24
D45V5, multiclass
        clus
vv       SLITRK6 MUTATED SLITRK6 WILD-TYPE
  CLUS_1               8                69
  CLUS_2               0                25
  CLUS_3               2                12
D45V6, multiclass
        clus
vv       SLITRK6 MUTATED SLITRK6 WILD-TYPE
  CLUS_1               3                23
  CLUS_2               0                23
  CLUS_3               7                60

Clustering(46) Variable = TP53TG5 MUTATION ANALYSIS
D46V1, multiclass
        clus
vv       TP53TG5 MUTATED TP53TG5 WILD-TYPE
  CLUS_1               0                47
  CLUS_2               0                15
  CLUS_3               2                 8
  CLUS_4               2                41
D46V2, multiclass
[1] "Remove cluster labels:" "TP53TG5 MUTATED"       
clus
  TP53TG5 MUTATED TP53TG5 WILD-TYPE 
                2                66 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6453 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-BR-6458        TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6709 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-BR-6852        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5813 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
D46V3, multiclass
D46V4, multiclass
        clus
vv       TP53TG5 MUTATED TP53TG5 WILD-TYPE
  CLUS_1               1                31
  CLUS_2               1                46
  CLUS_3               1                24
D46V5, multiclass
        clus
vv       TP53TG5 MUTATED TP53TG5 WILD-TYPE
  CLUS_1               3                74
  CLUS_2               1                24
  CLUS_3               0                14
D46V6, multiclass
        clus
vv       TP53TG5 MUTATED TP53TG5 WILD-TYPE
  CLUS_1               0                26
  CLUS_2               1                22
  CLUS_3               3                64

Clustering(47) Variable = LHCGR MUTATION ANALYSIS
D47V1, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             3              44
  CLUS_2             1              14
  CLUS_3             0              10
  CLUS_4             3              40
D47V2, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             1               8
  CLUS_2             1              13
  CLUS_3             1              21
  CLUS_4             1              22
D47V3, multiclass
D47V4, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             1              31
  CLUS_2             2              45
  CLUS_3             2              23
D47V5, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             4              73
  CLUS_2             2              23
  CLUS_3             1              13
D47V6, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             1              25
  CLUS_2             3              20
  CLUS_3             3              64
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"          "MRNASEQ_CNMF" 
                     V4                      V5                      V6 
"MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
