
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/335601/STAD-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/STAD-TP/2667074/1.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=257, 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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=2,	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=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=2, 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             8              12
  CLUS_2             1              54
  CLUS_3             5              35
D1V2, multiclass
        clus
vv       CBWD1 MUTATED CBWD1 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             3              11
  CLUS_3             1              24
  CLUS_4             0              20
D1V3, binary
                 cls
clus               0  1
  CBWD1 MUTATED    6  3
  CBWD1 WILD-TYPE 16 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBWD1 MUTATED      6    3
  CBWD1 WILD-TYPE   16   18
        clus
vv       CBWD1 MUTATED CBWD1 WILD-TYPE
  CLUS_1             6              16
  CLUS_2             3              18
D1V4, multiclass
        clus
vv       CBWD1 MUTATED CBWD1 WILD-TYPE
  CLUS_1             1              14
  CLUS_2             2               5
  CLUS_3             6              15
D1V5, multiclass
        clus
vv       CBWD1 MUTATED CBWD1 WILD-TYPE
  CLUS_1            13              65
  CLUS_2             0              24
  CLUS_3             1              12
D1V6, multiclass
        clus
vv       CBWD1 MUTATED CBWD1 WILD-TYPE
  CLUS_1             1              26
  CLUS_2            10              46
  CLUS_3             3              29

Clustering(2) Variable = KRAS MUTATION ANALYSIS
D2V1, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            5             15
  CLUS_2            4             51
  CLUS_3            5             35
D2V2, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            0              9
  CLUS_2            0             14
  CLUS_3            4             21
  CLUS_4            2             18
D2V3, binary
                cls
clus              0  1
  KRAS MUTATED    4  3
  KRAS WILD-TYPE 18 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      4    3
  KRAS WILD-TYPE   18   18
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            4             18
  CLUS_2            3             18
D2V4, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            1             14
  CLUS_2            2              5
  CLUS_3            4             17
D2V5, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1           12             66
  CLUS_2            2             22
  CLUS_3            0             13
D2V6, multiclass
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  CLUS_1            2             25
  CLUS_2            8             48
  CLUS_3            4             28

Clustering(3) Variable = PGM5 MUTATION ANALYSIS
D3V1, multiclass
        clus
vv       PGM5 MUTATED PGM5 WILD-TYPE
  CLUS_1           10             10
  CLUS_2            2             53
  CLUS_3            4             36
D3V2, multiclass
        clus
vv       PGM5 MUTATED PGM5 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            5              9
  CLUS_3            1             24
  CLUS_4            0             20
D3V3, binary
                cls
clus              0  1
  PGM5 MUTATED    7  3
  PGM5 WILD-TYPE 15 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM5 MUTATED      7    3
  PGM5 WILD-TYPE   15   18
        clus
vv       PGM5 MUTATED PGM5 WILD-TYPE
  CLUS_1            7             15
  CLUS_2            3             18
D3V4, multiclass
        clus
vv       PGM5 MUTATED PGM5 WILD-TYPE
  CLUS_1            1             14
  CLUS_2            2              5
  CLUS_3            7             14
D3V5, multiclass
        clus
vv       PGM5 MUTATED PGM5 WILD-TYPE
  CLUS_1           14             64
  CLUS_2            1             23
  CLUS_3            1             12
D3V6, multiclass
        clus
vv       PGM5 MUTATED PGM5 WILD-TYPE
  CLUS_1            1             26
  CLUS_2           11             45
  CLUS_3            4             28

Clustering(4) Variable = RPL22 MUTATION ANALYSIS
D4V1, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             4              16
  CLUS_2             1              54
  CLUS_3             4              36
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, binary
                 cls
clus               0  1
  RPL22 MUTATED    2  4
  RPL22 WILD-TYPE 20 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL22 MUTATED      2    4
  RPL22 WILD-TYPE   20   17
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             2              20
  CLUS_2             4              17
D4V4, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             1              14
  CLUS_2             3               4
  CLUS_3             2              19
D4V5, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             8              70
  CLUS_2             0              24
  CLUS_3             1              12
D4V6, multiclass
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  CLUS_1             1              26
  CLUS_2             7              49
  CLUS_3             1              31

Clustering(5) Variable = TP53 MUTATION ANALYSIS
D5V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            4             16
  CLUS_2           36             19
  CLUS_3           11             29
D5V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2              7
  CLUS_2            6              8
  CLUS_3            9             16
  CLUS_4           15              5
D5V3, binary
                cls
clus              0  1
  TP53 MUTATED    9  8
  TP53 WILD-TYPE 13 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      9    8
  TP53 WILD-TYPE   13   13
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            9             13
  CLUS_2            8             13
D5V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8              7
  CLUS_2            1              6
  CLUS_3            8             13
D5V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           29             49
  CLUS_2           11             13
  CLUS_3           11              2
D5V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           22              5
  CLUS_2           20             36
  CLUS_3            9             23

Clustering(6) Variable = TRIM48 MUTATION ANALYSIS
D6V1, multiclass
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              4               16
  CLUS_2              1               54
  CLUS_3              5               35
D6V2, multiclass
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              2               12
  CLUS_3              1               24
  CLUS_4              0               20
D6V3, binary
                  cls
clus                0  1
  TRIM48 MUTATED    3  2
  TRIM48 WILD-TYPE 19 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM48 MUTATED      3    2
  TRIM48 WILD-TYPE   19   19
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              3               19
  CLUS_2              2               19
D6V4, multiclass
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              2               13
  CLUS_2              1                6
  CLUS_3              2               19
D6V5, multiclass
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1             10               68
  CLUS_2              0               24
  CLUS_3              0               13
D6V6, multiclass
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  CLUS_1              0               27
  CLUS_2              7               49
  CLUS_3              3               29

Clustering(7) Variable = XPOT MUTATION ANALYSIS
D7V1, multiclass
        clus
vv       XPOT MUTATED XPOT WILD-TYPE
  CLUS_1            3             17
  CLUS_2            0             55
  CLUS_3            3             37
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, binary
                cls
clus              0  1
  XPOT MUTATED    1  3
  XPOT WILD-TYPE 21 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPOT MUTATED      1    3
  XPOT WILD-TYPE   21   18
        clus
vv       XPOT MUTATED XPOT WILD-TYPE
  CLUS_1            1             21
  CLUS_2            3             18
D7V4, multiclass
        clus
vv       XPOT MUTATED XPOT WILD-TYPE
  CLUS_1            1             14
  CLUS_2            1              6
  CLUS_3            2             19
D7V5, multiclass
        clus
vv       XPOT MUTATED XPOT WILD-TYPE
  CLUS_1            6             72
  CLUS_2            0             24
  CLUS_3            0             13
D7V6, multiclass
        clus
vv       XPOT MUTATED XPOT WILD-TYPE
  CLUS_1            0             27
  CLUS_2            6             50
  CLUS_3            0             32

Clustering(8) Variable = PIK3CA MUTATION ANALYSIS
D8V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              9               11
  CLUS_2              4               51
  CLUS_3             11               29
D8V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              9                0
  CLUS_2              4               10
  CLUS_3              3               22
  CLUS_4              2               18
D8V3, binary
                  cls
clus                0  1
  PIK3CA MUTATED    2  4
  PIK3CA WILD-TYPE 20 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      2    4
  PIK3CA WILD-TYPE   20   17
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2               20
  CLUS_2              4               17
D8V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3               12
  CLUS_2              1                6
  CLUS_3              2               19
D8V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1             21               57
  CLUS_2              2               22
  CLUS_3              1               12
D8V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2               25
  CLUS_2             20               36
  CLUS_3              2               30

Clustering(9) Variable = ACVR2A MUTATION ANALYSIS
D9V1, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              4               16
  CLUS_2              0               55
  CLUS_3              9               31
D9V2, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              1                8
  CLUS_2              4               10
  CLUS_3              1               24
  CLUS_4              0               20
D9V3, binary
                  cls
clus                0  1
  ACVR2A MUTATED    3  4
  ACVR2A WILD-TYPE 19 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED      3    4
  ACVR2A WILD-TYPE   19   17
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              3               19
  CLUS_2              4               17
D9V4, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              3               12
  CLUS_2              2                5
  CLUS_3              2               19
D9V5, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1             13               65
  CLUS_2              0               24
  CLUS_3              0               13
D9V6, multiclass
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  CLUS_1              0               27
  CLUS_2              9               47
  CLUS_3              4               28

Clustering(10) Variable = RHOA MUTATION ANALYSIS
D10V1, multiclass
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  CLUS_1            0             20
  CLUS_2            2             53
  CLUS_3            5             35
D10V2, multiclass
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  CLUS_1            0              9
  CLUS_2            1             13
  CLUS_3            3             22
  CLUS_4            1             19
D10V3, binary
                cls
clus              0  1
  RHOA MUTATED    0  1
  RHOA WILD-TYPE 22 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      0    1
  RHOA WILD-TYPE   22   20
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  CLUS_1            0             22
  CLUS_2            1             20
D10V4, multiclass
[1] "Remove cluster labels:" "RHOA MUTATED"          
clus
  RHOA MUTATED RHOA WILD-TYPE 
             1             42 
    TCGA-BR-4187     TCGA-BR-4191     TCGA-BR-4201     TCGA-BR-4253 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-BR-4255     TCGA-BR-4256     TCGA-BR-4257     TCGA-BR-4267 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-BR-4279     TCGA-BR-4280     TCGA-BR-4292     TCGA-BR-4294 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-BR-4357     TCGA-BR-4361     TCGA-BR-4362     TCGA-BR-4363 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-BR-4366     TCGA-BR-4367     TCGA-BR-4368     TCGA-BR-4369 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-BR-4370     TCGA-BR-4371     TCGA-CG-4301     TCGA-CG-4304 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-CG-4305     TCGA-CG-4306     TCGA-CG-4436     TCGA-CG-4438 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-CG-4440     TCGA-CG-4442     TCGA-CG-4443     TCGA-CG-4444 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-CG-4449     TCGA-CG-4460     TCGA-CG-4462     TCGA-CG-4466 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-CG-4469     TCGA-CG-4472     TCGA-CG-4474     TCGA-CG-4475 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" "RHOA WILD-TYPE" 
    TCGA-CG-4476     TCGA-CG-4477 
"RHOA WILD-TYPE" "RHOA WILD-TYPE" 
D10V5, multiclass
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  CLUS_1            4             74
  CLUS_2            3             21
  CLUS_3            0             13
D10V6, multiclass
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  CLUS_1            1             26
  CLUS_2            3             53
  CLUS_3            3             29

Clustering(11) Variable = ARID1A MUTATION ANALYSIS
D11V1, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             10               10
  CLUS_2              3               52
  CLUS_3              9               31
D11V2, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              4                5
  CLUS_2              2               12
  CLUS_3              4               21
  CLUS_4              0               20
D11V3, binary
                  cls
clus                0  1
  ARID1A MUTATED    4  6
  ARID1A WILD-TYPE 18 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      4    6
  ARID1A WILD-TYPE   18   15
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              4               18
  CLUS_2              6               15
D11V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              4               11
  CLUS_2              3                4
  CLUS_3              3               18
D11V5, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1             21               57
  CLUS_2              1               23
  CLUS_3              0               13
D11V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0               27
  CLUS_2             18               38
  CLUS_3              4               28

Clustering(12) Variable = OR8H3 MUTATION ANALYSIS
D12V1, multiclass
        clus
vv       OR8H3 MUTATED OR8H3 WILD-TYPE
  CLUS_1             2              18
  CLUS_2             6              49
  CLUS_3             2              38
D12V2, multiclass
        clus
vv       OR8H3 MUTATED OR8H3 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             4              10
  CLUS_3             1              24
  CLUS_4             1              19
D12V3, binary
                 cls
clus               0  1
  OR8H3 MUTATED    0  3
  OR8H3 WILD-TYPE 22 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8H3 MUTATED      0    3
  OR8H3 WILD-TYPE   22   18
        clus
vv       OR8H3 MUTATED OR8H3 WILD-TYPE
  CLUS_1             0              22
  CLUS_2             3              18
D12V4, multiclass
        clus
vv       OR8H3 MUTATED OR8H3 WILD-TYPE
  CLUS_1             3              12
  CLUS_2             0               7
  CLUS_3             0              21
D12V5, multiclass
        clus
vv       OR8H3 MUTATED OR8H3 WILD-TYPE
  CLUS_1             8              70
  CLUS_2             1              23
  CLUS_3             1              12
D12V6, multiclass
        clus
vv       OR8H3 MUTATED OR8H3 WILD-TYPE
  CLUS_1             1              26
  CLUS_2             8              48
  CLUS_3             1              31

Clustering(13) Variable = EDNRB MUTATION ANALYSIS
D13V1, multiclass
        clus
vv       EDNRB MUTATED EDNRB WILD-TYPE
  CLUS_1             4              16
  CLUS_2             5              50
  CLUS_3             3              37
D13V2, multiclass
        clus
vv       EDNRB MUTATED EDNRB WILD-TYPE
  CLUS_1             0               9
  CLUS_2             2              12
  CLUS_3             1              24
  CLUS_4             1              19
D13V3, binary
                 cls
clus               0  1
  EDNRB MUTATED    2  4
  EDNRB WILD-TYPE 20 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EDNRB MUTATED      2    4
  EDNRB WILD-TYPE   20   17
        clus
vv       EDNRB MUTATED EDNRB WILD-TYPE
  CLUS_1             2              20
  CLUS_2             4              17
D13V4, multiclass
        clus
vv       EDNRB MUTATED EDNRB WILD-TYPE
  CLUS_1             3              12
  CLUS_2             1               6
  CLUS_3             2              19
D13V5, multiclass
        clus
vv       EDNRB MUTATED EDNRB WILD-TYPE
  CLUS_1             9              69
  CLUS_2             1              23
  CLUS_3             2              11
D13V6, multiclass
        clus
vv       EDNRB MUTATED EDNRB WILD-TYPE
  CLUS_1             2              25
  CLUS_2             9              47
  CLUS_3             1              31

Clustering(14) Variable = ZNF804B MUTATION ANALYSIS
D14V1, multiclass
        clus
vv       ZNF804B MUTATED ZNF804B WILD-TYPE
  CLUS_1               4                16
  CLUS_2              11                44
  CLUS_3               3                37
D14V2, multiclass
        clus
vv       ZNF804B MUTATED ZNF804B WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               5                 9
  CLUS_3               3                22
  CLUS_4               1                19
D14V3, binary
                   cls
clus                 0  1
  ZNF804B MUTATED    3  6
  ZNF804B WILD-TYPE 19 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF804B MUTATED      3    6
  ZNF804B WILD-TYPE   19   15
        clus
vv       ZNF804B MUTATED ZNF804B WILD-TYPE
  CLUS_1               3                19
  CLUS_2               6                15
D14V4, multiclass
        clus
vv       ZNF804B MUTATED ZNF804B WILD-TYPE
  CLUS_1               4                11
  CLUS_2               1                 6
  CLUS_3               4                17
D14V5, multiclass
        clus
vv       ZNF804B MUTATED ZNF804B WILD-TYPE
  CLUS_1              14                64
  CLUS_2               1                23
  CLUS_3               3                10
D14V6, multiclass
        clus
vv       ZNF804B MUTATED ZNF804B WILD-TYPE
  CLUS_1               5                22
  CLUS_2              11                45
  CLUS_3               2                30

Clustering(15) Variable = IRF2 MUTATION ANALYSIS
D15V1, multiclass
        clus
vv       IRF2 MUTATED IRF2 WILD-TYPE
  CLUS_1            6             14
  CLUS_2            0             55
  CLUS_3            2             38
D15V2, multiclass
        clus
vv       IRF2 MUTATED IRF2 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            2             12
  CLUS_3            0             25
  CLUS_4            0             20
D15V3, binary
                cls
clus              0  1
  IRF2 MUTATED    2  2
  IRF2 WILD-TYPE 20 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF2 MUTATED      2    2
  IRF2 WILD-TYPE   20   19
        clus
vv       IRF2 MUTATED IRF2 WILD-TYPE
  CLUS_1            2             20
  CLUS_2            2             19
D15V4, multiclass
        clus
vv       IRF2 MUTATED IRF2 WILD-TYPE
  CLUS_1            0             15
  CLUS_2            1              6
  CLUS_3            3             18
D15V5, multiclass
        clus
vv       IRF2 MUTATED IRF2 WILD-TYPE
  CLUS_1            8             70
  CLUS_2            0             24
  CLUS_3            0             13
D15V6, multiclass
        clus
vv       IRF2 MUTATED IRF2 WILD-TYPE
  CLUS_1            0             27
  CLUS_2            5             51
  CLUS_3            3             29

Clustering(16) Variable = IAPP MUTATION ANALYSIS
D16V1, multiclass
        clus
vv       IAPP MUTATED IAPP WILD-TYPE
  CLUS_1            0             20
  CLUS_2            1             54
  CLUS_3            3             37
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, binary
                cls
clus              0  1
  IAPP MUTATED    1  1
  IAPP WILD-TYPE 21 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  IAPP MUTATED      1    1
  IAPP WILD-TYPE   21   20
        clus
vv       IAPP MUTATED IAPP WILD-TYPE
  CLUS_1            1             21
  CLUS_2            1             20
D16V4, multiclass
[1] "Remove cluster labels:" "IAPP MUTATED"          
clus
  IAPP MUTATED IAPP WILD-TYPE 
             2             41 
    TCGA-BR-4187     TCGA-BR-4191     TCGA-BR-4201     TCGA-BR-4253 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-BR-4255     TCGA-BR-4257     TCGA-BR-4267     TCGA-BR-4279 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-BR-4280     TCGA-BR-4292     TCGA-BR-4294     TCGA-BR-4357 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-BR-4361     TCGA-BR-4362     TCGA-BR-4363     TCGA-BR-4366 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-BR-4367     TCGA-BR-4368     TCGA-BR-4369     TCGA-BR-4370 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-BR-4371     TCGA-CG-4301     TCGA-CG-4304     TCGA-CG-4305 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-CG-4306     TCGA-CG-4436     TCGA-CG-4438     TCGA-CG-4440 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-CG-4442     TCGA-CG-4443     TCGA-CG-4444     TCGA-CG-4449 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-CG-4460     TCGA-CG-4462     TCGA-CG-4465     TCGA-CG-4469 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-CG-4472     TCGA-CG-4474     TCGA-CG-4475     TCGA-CG-4476 
"IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" "IAPP WILD-TYPE" 
    TCGA-CG-4477 
"IAPP WILD-TYPE" 
D16V5, multiclass
        clus
vv       IAPP MUTATED IAPP WILD-TYPE
  CLUS_1            1             77
  CLUS_2            2             22
  CLUS_3            1             12
D16V6, multiclass
        clus
vv       IAPP MUTATED IAPP WILD-TYPE
  CLUS_1            1             26
  CLUS_2            1             55
  CLUS_3            2             30

Clustering(17) Variable = PCDH15 MUTATION ANALYSIS
D17V1, multiclass
        clus
vv       PCDH15 MUTATED PCDH15 WILD-TYPE
  CLUS_1              3               17
  CLUS_2              9               46
  CLUS_3              9               31
D17V2, multiclass
        clus
vv       PCDH15 MUTATED PCDH15 WILD-TYPE
  CLUS_1              2                7
  CLUS_2              2               12
  CLUS_3              5               20
  CLUS_4              3               17
D17V3, binary
                  cls
clus                0  1
  PCDH15 MUTATED    4  5
  PCDH15 WILD-TYPE 18 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH15 MUTATED      4    5
  PCDH15 WILD-TYPE   18   16
        clus
vv       PCDH15 MUTATED PCDH15 WILD-TYPE
  CLUS_1              4               18
  CLUS_2              5               16
D17V4, multiclass
        clus
vv       PCDH15 MUTATED PCDH15 WILD-TYPE
  CLUS_1              4               11
  CLUS_2              1                6
  CLUS_3              4               17
D17V5, multiclass
        clus
vv       PCDH15 MUTATED PCDH15 WILD-TYPE
  CLUS_1             16               62
  CLUS_2              3               21
  CLUS_3              3               10
D17V6, multiclass
        clus
vv       PCDH15 MUTATED PCDH15 WILD-TYPE
  CLUS_1              5               22
  CLUS_2             10               46
  CLUS_3              7               25

Clustering(18) Variable = SPRYD5 MUTATION ANALYSIS
D18V1, multiclass
        clus
vv       SPRYD5 MUTATED SPRYD5 WILD-TYPE
  CLUS_1              3               17
  CLUS_2              2               53
  CLUS_3              3               37
D18V2, multiclass
        clus
vv       SPRYD5 MUTATED SPRYD5 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              3               11
  CLUS_3              1               24
  CLUS_4              0               20
D18V3, binary
                  cls
clus                0  1
  SPRYD5 MUTATED    2  2
  SPRYD5 WILD-TYPE 20 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPRYD5 MUTATED      2    2
  SPRYD5 WILD-TYPE   20   19
        clus
vv       SPRYD5 MUTATED SPRYD5 WILD-TYPE
  CLUS_1              2               20
  CLUS_2              2               19
D18V4, multiclass
        clus
vv       SPRYD5 MUTATED SPRYD5 WILD-TYPE
  CLUS_1              1               14
  CLUS_2              0                7
  CLUS_3              3               18
D18V5, multiclass
        clus
vv       SPRYD5 MUTATED SPRYD5 WILD-TYPE
  CLUS_1              7               71
  CLUS_2              0               24
  CLUS_3              1               12
D18V6, multiclass
        clus
vv       SPRYD5 MUTATED SPRYD5 WILD-TYPE
  CLUS_1              1               26
  CLUS_2              4               52
  CLUS_3              3               29

Clustering(19) Variable = TUSC3 MUTATION ANALYSIS
D19V1, multiclass
        clus
vv       TUSC3 MUTATED TUSC3 WILD-TYPE
  CLUS_1             2              18
  CLUS_2             2              53
  CLUS_3             5              35
D19V2, multiclass
        clus
vv       TUSC3 MUTATED TUSC3 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             1              13
  CLUS_3             4              21
  CLUS_4             1              19
D19V3, binary
                 cls
clus               0  1
  TUSC3 MUTATED    2  0
  TUSC3 WILD-TYPE 20 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUSC3 MUTATED      2    0
  TUSC3 WILD-TYPE   20   21
        clus
vv       TUSC3 MUTATED TUSC3 WILD-TYPE
  CLUS_1             2              20
  CLUS_2             0              21
D19V4, multiclass
[1] "Remove cluster labels:" "TUSC3 MUTATED"         
clus
  TUSC3 MUTATED TUSC3 WILD-TYPE 
              2              41 
     TCGA-BR-4187      TCGA-BR-4191      TCGA-BR-4201      TCGA-BR-4253 
"TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" 
     TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4257      TCGA-BR-4267 
"TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" 
     TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292      TCGA-BR-4294 
"TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" 
     TCGA-BR-4357      TCGA-BR-4362      TCGA-BR-4363      TCGA-BR-4366 
"TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" 
     TCGA-BR-4367      TCGA-BR-4368      TCGA-BR-4369      TCGA-BR-4370 
"TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" 
     TCGA-BR-4371      TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305 
"TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" 
     TCGA-CG-4306      TCGA-CG-4436      TCGA-CG-4438      TCGA-CG-4440 
"TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" 
     TCGA-CG-4442      TCGA-CG-4443      TCGA-CG-4444      TCGA-CG-4449 
"TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" 
     TCGA-CG-4462      TCGA-CG-4465      TCGA-CG-4466      TCGA-CG-4469 
"TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" 
     TCGA-CG-4472      TCGA-CG-4474      TCGA-CG-4475      TCGA-CG-4476 
"TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" "TUSC3 WILD-TYPE" 
     TCGA-CG-4477 
"TUSC3 WILD-TYPE" 
D19V5, multiclass
        clus
vv       TUSC3 MUTATED TUSC3 WILD-TYPE
  CLUS_1             6              72
  CLUS_2             2              22
  CLUS_3             1              12
D19V6, multiclass
        clus
vv       TUSC3 MUTATED TUSC3 WILD-TYPE
  CLUS_1             3              24
  CLUS_2             4              52
  CLUS_3             2              30

Clustering(20) Variable = FGF22 MUTATION ANALYSIS
D20V1, multiclass
        clus
vv       FGF22 MUTATED FGF22 WILD-TYPE
  CLUS_1             2              18
  CLUS_2             0              55
  CLUS_3             1              39
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, binary
                 cls
clus               0  1
  FGF22 MUTATED    1  1
  FGF22 WILD-TYPE 21 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGF22 MUTATED      1    1
  FGF22 WILD-TYPE   21   20
        clus
vv       FGF22 MUTATED FGF22 WILD-TYPE
  CLUS_1             1              21
  CLUS_2             1              20
D20V4, multiclass
[1] "Remove cluster labels:" "FGF22 MUTATED"         
clus
  FGF22 MUTATED FGF22 WILD-TYPE 
              2              41 
     TCGA-BR-4187      TCGA-BR-4191      TCGA-BR-4201      TCGA-BR-4253 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4267      TCGA-BR-4279 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-BR-4280      TCGA-BR-4292      TCGA-BR-4294      TCGA-BR-4357 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-BR-4361      TCGA-BR-4362      TCGA-BR-4363      TCGA-BR-4366 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-BR-4367      TCGA-BR-4368      TCGA-BR-4369      TCGA-BR-4370 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-BR-4371      TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-CG-4436      TCGA-CG-4438      TCGA-CG-4440      TCGA-CG-4442 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-CG-4443      TCGA-CG-4444      TCGA-CG-4449      TCGA-CG-4460 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-CG-4462      TCGA-CG-4465      TCGA-CG-4466      TCGA-CG-4469 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-CG-4472      TCGA-CG-4474      TCGA-CG-4475      TCGA-CG-4476 
"FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" "FGF22 WILD-TYPE" 
     TCGA-CG-4477 
"FGF22 WILD-TYPE" 
D20V5, multiclass
        clus
vv       FGF22 MUTATED FGF22 WILD-TYPE
  CLUS_1             3              75
  CLUS_2             0              24
  CLUS_3             0              13
D20V6, multiclass
        clus
vv       FGF22 MUTATED FGF22 WILD-TYPE
  CLUS_1             0              27
  CLUS_2             3              53
  CLUS_3             0              32

Clustering(21) Variable = HLA-B MUTATION ANALYSIS
D21V1, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             3              17
  CLUS_2             1              54
  CLUS_3             5              35
D21V2, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             2               7
  CLUS_2             3              11
  CLUS_3             0              25
  CLUS_4             0              20
D21V3, binary
                 cls
clus               0  1
  HLA-B MUTATED    3  1
  HLA-B WILD-TYPE 19 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      3    1
  HLA-B WILD-TYPE   19   20
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             3              19
  CLUS_2             1              20
D21V4, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             1              14
  CLUS_2             1               6
  CLUS_3             2              19
D21V5, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             7              71
  CLUS_2             1              23
  CLUS_3             1              12
D21V6, multiclass
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  CLUS_1             1              26
  CLUS_2             6              50
  CLUS_3             2              30

Clustering(22) Variable = PTH2 MUTATION ANALYSIS
D22V1, multiclass
        clus
vv       PTH2 MUTATED PTH2 WILD-TYPE
  CLUS_1            0             20
  CLUS_2            2             53
  CLUS_3            1             39
D22V2, multiclass
        clus
vv       PTH2 MUTATED PTH2 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            0             14
  CLUS_3            0             25
  CLUS_4            2             18
D22V3, binary
                cls
clus              0  1
  PTH2 MUTATED    0  0
  PTH2 WILD-TYPE 22 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTH2 MUTATED      0    0
  PTH2 WILD-TYPE   22   21
D22V4, multiclass
D22V5, multiclass
        clus
vv       PTH2 MUTATED PTH2 WILD-TYPE
  CLUS_1            1             77
  CLUS_2            2             22
  CLUS_3            0             13
D22V6, multiclass
        clus
vv       PTH2 MUTATED PTH2 WILD-TYPE
  CLUS_1            1             26
  CLUS_2            1             55
  CLUS_3            1             31

Clustering(23) Variable = C17ORF63 MUTATION ANALYSIS
D23V1, multiclass
        clus
vv       C17ORF63 MUTATED C17ORF63 WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                1                 54
  CLUS_3                1                 39
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, binary
                    cls
clus                  0  1
  C17ORF63 MUTATED    1  1
  C17ORF63 WILD-TYPE 21 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF63 MUTATED      1    1
  C17ORF63 WILD-TYPE   21   20
        clus
vv       C17ORF63 MUTATED C17ORF63 WILD-TYPE
  CLUS_1                1                 21
  CLUS_2                1                 20
D23V4, multiclass
[1] "Remove cluster labels:" "C17ORF63 MUTATED"      
clus
  C17ORF63 MUTATED C17ORF63 WILD-TYPE 
                 2                 41 
        TCGA-BR-4187         TCGA-BR-4191         TCGA-BR-4201 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-BR-4253         TCGA-BR-4255         TCGA-BR-4256 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-BR-4257         TCGA-BR-4267         TCGA-BR-4279 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-BR-4280         TCGA-BR-4292         TCGA-BR-4294 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-BR-4357         TCGA-BR-4361         TCGA-BR-4362 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-BR-4363         TCGA-BR-4366         TCGA-BR-4367 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-BR-4369         TCGA-BR-4370         TCGA-BR-4371 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4438         TCGA-CG-4440 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-CG-4442         TCGA-CG-4443         TCGA-CG-4444 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4460         TCGA-CG-4462 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4475 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
        TCGA-CG-4476         TCGA-CG-4477 
"C17ORF63 WILD-TYPE" "C17ORF63 WILD-TYPE" 
D23V5, multiclass
        clus
vv       C17ORF63 MUTATED C17ORF63 WILD-TYPE
  CLUS_1                3                 75
  CLUS_2                0                 24
  CLUS_3                0                 13
D23V6, multiclass
        clus
vv       C17ORF63 MUTATED C17ORF63 WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                2                 54
  CLUS_3                1                 31

Clustering(24) Variable = SMAD4 MUTATION ANALYSIS
D24V1, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             0              20
  CLUS_2             5              50
  CLUS_3             2              38
D24V2, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             0              14
  CLUS_3             1              24
  CLUS_4             2              18
D24V3, binary
                 cls
clus               0  1
  SMAD4 MUTATED    2  1
  SMAD4 WILD-TYPE 20 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      2    1
  SMAD4 WILD-TYPE   20   20
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             2              20
  CLUS_2             1              20
D24V4, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             1              14
  CLUS_2             1               6
  CLUS_3             1              20
D24V5, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             6              72
  CLUS_2             1              23
  CLUS_3             0              13
D24V6, multiclass
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  CLUS_1             1              26
  CLUS_2             4              52
  CLUS_3             2              30

Clustering(25) Variable = POTEG MUTATION ANALYSIS
D25V1, multiclass
        clus
vv       POTEG MUTATED POTEG WILD-TYPE
  CLUS_1             1              19
  CLUS_2             1              54
  CLUS_3             4              36
D25V2, multiclass
        clus
vv       POTEG MUTATED POTEG WILD-TYPE
  CLUS_1             0               9
  CLUS_2             1              13
  CLUS_3             2              23
  CLUS_4             0              20
D25V3, binary
                 cls
clus               0  1
  POTEG MUTATED    2  1
  POTEG WILD-TYPE 20 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEG MUTATED      2    1
  POTEG WILD-TYPE   20   20
        clus
vv       POTEG MUTATED POTEG WILD-TYPE
  CLUS_1             2              20
  CLUS_2             1              20
D25V4, multiclass
        clus
vv       POTEG MUTATED POTEG WILD-TYPE
  CLUS_1             1              14
  CLUS_2             0               7
  CLUS_3             2              19
D25V5, multiclass
        clus
vv       POTEG MUTATED POTEG WILD-TYPE
  CLUS_1             4              74
  CLUS_2             2              22
  CLUS_3             0              13
D25V6, multiclass
        clus
vv       POTEG MUTATED POTEG WILD-TYPE
  CLUS_1             0              27
  CLUS_2             3              53
  CLUS_3             3              29

Clustering(26) Variable = RNF43 MUTATION ANALYSIS
D26V1, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             8              12
  CLUS_2             1              54
  CLUS_3             4              36
D26V2, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             4              10
  CLUS_3             2              23
  CLUS_4             0              20
D26V3, binary
                 cls
clus               0  1
  RNF43 MUTATED    3  4
  RNF43 WILD-TYPE 19 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      3    4
  RNF43 WILD-TYPE   19   17
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             3              19
  CLUS_2             4              17
D26V4, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             2              13
  CLUS_2             2               5
  CLUS_3             3              18
D26V5, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1            12              66
  CLUS_2             1              23
  CLUS_3             0              13
D26V6, multiclass
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  CLUS_1             0              27
  CLUS_2             7              49
  CLUS_3             6              26

Clustering(27) Variable = WBSCR17 MUTATION ANALYSIS
D27V1, multiclass
        clus
vv       WBSCR17 MUTATED WBSCR17 WILD-TYPE
  CLUS_1               5                15
  CLUS_2               3                52
  CLUS_3               4                36
D27V2, multiclass
        clus
vv       WBSCR17 MUTATED WBSCR17 WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               5                 9
  CLUS_3               2                23
  CLUS_4               0                20
D27V3, binary
                   cls
clus                 0  1
  WBSCR17 MUTATED    3  1
  WBSCR17 WILD-TYPE 19 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WBSCR17 MUTATED      3    1
  WBSCR17 WILD-TYPE   19   20
        clus
vv       WBSCR17 MUTATED WBSCR17 WILD-TYPE
  CLUS_1               3                19
  CLUS_2               1                20
D27V4, multiclass
        clus
vv       WBSCR17 MUTATED WBSCR17 WILD-TYPE
  CLUS_1               1                14
  CLUS_2               0                 7
  CLUS_3               3                18
D27V5, multiclass
        clus
vv       WBSCR17 MUTATED WBSCR17 WILD-TYPE
  CLUS_1              11                67
  CLUS_2               1                23
  CLUS_3               0                13
D27V6, multiclass
        clus
vv       WBSCR17 MUTATED WBSCR17 WILD-TYPE
  CLUS_1               1                26
  CLUS_2               7                49
  CLUS_3               4                28

Clustering(28) Variable = PHF2 MUTATION ANALYSIS
D28V1, multiclass
        clus
vv       PHF2 MUTATED PHF2 WILD-TYPE
  CLUS_1            6             14
  CLUS_2            0             55
  CLUS_3            6             34
D28V2, multiclass
        clus
vv       PHF2 MUTATED PHF2 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            4             10
  CLUS_3            1             24
  CLUS_4            0             20
D28V3, binary
                cls
clus              0  1
  PHF2 MUTATED    2  3
  PHF2 WILD-TYPE 20 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF2 MUTATED      2    3
  PHF2 WILD-TYPE   20   18
        clus
vv       PHF2 MUTATED PHF2 WILD-TYPE
  CLUS_1            2             20
  CLUS_2            3             18
D28V4, multiclass
        clus
vv       PHF2 MUTATED PHF2 WILD-TYPE
  CLUS_1            1             14
  CLUS_2            3              4
  CLUS_3            1             20
D28V5, multiclass
        clus
vv       PHF2 MUTATED PHF2 WILD-TYPE
  CLUS_1           12             66
  CLUS_2            0             24
  CLUS_3            0             13
D28V6, multiclass
        clus
vv       PHF2 MUTATED PHF2 WILD-TYPE
  CLUS_1            0             27
  CLUS_2           10             46
  CLUS_3            2             30

Clustering(29) Variable = TPTE MUTATION ANALYSIS
D29V1, multiclass
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1            3             17
  CLUS_2            7             48
  CLUS_3            4             36
D29V2, multiclass
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1            1              8
  CLUS_2            1             13
  CLUS_3            2             23
  CLUS_4            3             17
D29V3, binary
                cls
clus              0  1
  TPTE MUTATED    2  4
  TPTE WILD-TYPE 20 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPTE MUTATED      2    4
  TPTE WILD-TYPE   20   17
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1            2             20
  CLUS_2            4             17
D29V4, multiclass
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1            3             12
  CLUS_2            1              6
  CLUS_3            2             19
D29V5, multiclass
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1           10             68
  CLUS_2            1             23
  CLUS_3            3             10
D29V6, multiclass
        clus
vv       TPTE MUTATED TPTE WILD-TYPE
  CLUS_1            4             23
  CLUS_2            8             48
  CLUS_3            2             30

Clustering(30) Variable = CDH1 MUTATION ANALYSIS
D30V1, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            2             18
  CLUS_2            2             53
  CLUS_3            6             34
D30V2, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            0              9
  CLUS_2            2             12
  CLUS_3            4             21
  CLUS_4            1             19
D30V3, binary
                cls
clus              0  1
  CDH1 MUTATED    1  2
  CDH1 WILD-TYPE 21 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED      1    2
  CDH1 WILD-TYPE   21   19
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            1             21
  CLUS_2            2             19
D30V4, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            2             13
  CLUS_2            0              7
  CLUS_3            1             20
D30V5, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            6             72
  CLUS_2            5             19
  CLUS_3            0             13
D30V6, multiclass
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  CLUS_1            0             27
  CLUS_2            6             50
  CLUS_3            5             27

Clustering(31) Variable = CPS1 MUTATION ANALYSIS
D31V1, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            4             16
  CLUS_2            5             50
  CLUS_3            4             36
D31V2, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            2             12
  CLUS_3            2             23
  CLUS_4            0             20
D31V3, binary
                cls
clus              0  1
  CPS1 MUTATED    4  3
  CPS1 WILD-TYPE 18 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED      4    3
  CPS1 WILD-TYPE   18   18
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            4             18
  CLUS_2            3             18
D31V4, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            3             12
  CLUS_2            1              6
  CLUS_3            3             18
D31V5, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1           10             68
  CLUS_2            2             22
  CLUS_3            1             12
D31V6, multiclass
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  CLUS_1            1             26
  CLUS_2           10             46
  CLUS_3            2             30

Clustering(32) Variable = INO80E MUTATION ANALYSIS
D32V1, multiclass
        clus
vv       INO80E MUTATED INO80E WILD-TYPE
  CLUS_1              2               18
  CLUS_2              1               54
  CLUS_3              2               38
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, binary
                  cls
clus                0  1
  INO80E MUTATED    3  1
  INO80E WILD-TYPE 19 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INO80E MUTATED      3    1
  INO80E WILD-TYPE   19   20
        clus
vv       INO80E MUTATED INO80E WILD-TYPE
  CLUS_1              3               19
  CLUS_2              1               20
D32V4, multiclass
        clus
vv       INO80E MUTATED INO80E WILD-TYPE
  CLUS_1              0               15
  CLUS_2              1                6
  CLUS_3              3               18
D32V5, multiclass
        clus
vv       INO80E MUTATED INO80E WILD-TYPE
  CLUS_1              4               74
  CLUS_2              0               24
  CLUS_3              1               12
D32V6, multiclass
        clus
vv       INO80E MUTATED INO80E WILD-TYPE
  CLUS_1              1               26
  CLUS_2              3               53
  CLUS_3              1               31

Clustering(33) Variable = ELF3 MUTATION ANALYSIS
D33V1, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            2             18
  CLUS_2            0             55
  CLUS_3            3             37
D33V2, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            1              8
  CLUS_2            2             12
  CLUS_3            1             24
  CLUS_4            0             20
D33V3, binary
                cls
clus              0  1
  ELF3 MUTATED    1  0
  ELF3 WILD-TYPE 21 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      1    0
  ELF3 WILD-TYPE   21   21
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            1             21
  CLUS_2            0             21
D33V4, multiclass
[1] "Remove cluster labels:" "ELF3 MUTATED"          
clus
  ELF3 MUTATED ELF3 WILD-TYPE 
             1             42 
    TCGA-BR-4187     TCGA-BR-4191     TCGA-BR-4201     TCGA-BR-4253 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-BR-4255     TCGA-BR-4256     TCGA-BR-4257     TCGA-BR-4267 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-BR-4279     TCGA-BR-4280     TCGA-BR-4292     TCGA-BR-4294 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-BR-4357     TCGA-BR-4362     TCGA-BR-4363     TCGA-BR-4366 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-BR-4367     TCGA-BR-4368     TCGA-BR-4369     TCGA-BR-4370 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-BR-4371     TCGA-CG-4301     TCGA-CG-4304     TCGA-CG-4305 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-CG-4306     TCGA-CG-4436     TCGA-CG-4438     TCGA-CG-4440 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-CG-4442     TCGA-CG-4443     TCGA-CG-4444     TCGA-CG-4449 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-CG-4460     TCGA-CG-4462     TCGA-CG-4465     TCGA-CG-4466 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-CG-4469     TCGA-CG-4472     TCGA-CG-4474     TCGA-CG-4475 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
    TCGA-CG-4476     TCGA-CG-4477 
"ELF3 WILD-TYPE" "ELF3 WILD-TYPE" 
D33V5, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            5             73
  CLUS_2            0             24
  CLUS_3            0             13
D33V6, multiclass
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  CLUS_1            0             27
  CLUS_2            5             51
  CLUS_3            0             32

Clustering(34) Variable = PARK2 MUTATION ANALYSIS
D34V1, multiclass
        clus
vv       PARK2 MUTATED PARK2 WILD-TYPE
  CLUS_1             4              16
  CLUS_2             2              53
  CLUS_3             3              37
D34V2, multiclass
        clus
vv       PARK2 MUTATED PARK2 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             3              11
  CLUS_3             0              25
  CLUS_4             1              19
D34V3, binary
                 cls
clus               0  1
  PARK2 MUTATED    3  2
  PARK2 WILD-TYPE 19 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARK2 MUTATED      3    2
  PARK2 WILD-TYPE   19   19
        clus
vv       PARK2 MUTATED PARK2 WILD-TYPE
  CLUS_1             3              19
  CLUS_2             2              19
D34V4, multiclass
        clus
vv       PARK2 MUTATED PARK2 WILD-TYPE
  CLUS_1             1              14
  CLUS_2             0               7
  CLUS_3             4              17
D34V5, multiclass
        clus
vv       PARK2 MUTATED PARK2 WILD-TYPE
  CLUS_1             7              71
  CLUS_2             1              23
  CLUS_3             1              12
D34V6, multiclass
        clus
vv       PARK2 MUTATED PARK2 WILD-TYPE
  CLUS_1             1              26
  CLUS_2             7              49
  CLUS_3             1              31

Clustering(35) Variable = LARP4B MUTATION ANALYSIS
D35V1, multiclass
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  CLUS_1              3               17
  CLUS_2              0               55
  CLUS_3              2               38
D35V2, multiclass
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  CLUS_1              0                9
  CLUS_2              2               12
  CLUS_3              1               24
  CLUS_4              0               20
D35V3, binary
                  cls
clus                0  1
  LARP4B MUTATED    1  1
  LARP4B WILD-TYPE 21 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED      1    1
  LARP4B WILD-TYPE   21   20
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  CLUS_1              1               21
  CLUS_2              1               20
D35V4, multiclass
[1] "Remove cluster labels:" "LARP4B MUTATED"        
clus
  LARP4B MUTATED LARP4B WILD-TYPE 
               2               41 
      TCGA-BR-4187       TCGA-BR-4191       TCGA-BR-4201       TCGA-BR-4253 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-BR-4255       TCGA-BR-4256       TCGA-BR-4257       TCGA-BR-4267 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4294       TCGA-BR-4357 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-BR-4362       TCGA-BR-4363       TCGA-BR-4366       TCGA-BR-4367 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-BR-4368       TCGA-BR-4369       TCGA-BR-4370       TCGA-BR-4371 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-CG-4301       TCGA-CG-4304       TCGA-CG-4305       TCGA-CG-4306 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-CG-4436       TCGA-CG-4438       TCGA-CG-4440       TCGA-CG-4442 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-CG-4443       TCGA-CG-4444       TCGA-CG-4449       TCGA-CG-4460 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-CG-4462       TCGA-CG-4465       TCGA-CG-4466       TCGA-CG-4469 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-CG-4472       TCGA-CG-4474       TCGA-CG-4475       TCGA-CG-4476 
"LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" "LARP4B WILD-TYPE" 
      TCGA-CG-4477 
"LARP4B WILD-TYPE" 
D35V5, multiclass
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  CLUS_1              5               73
  CLUS_2              0               24
  CLUS_3              0               13
D35V6, multiclass
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  CLUS_1              0               27
  CLUS_2              5               51
  CLUS_3              0               32

Clustering(36) Variable = OR6K3 MUTATION ANALYSIS
D36V1, multiclass
        clus
vv       OR6K3 MUTATED OR6K3 WILD-TYPE
  CLUS_1             3              17
  CLUS_2             1              54
  CLUS_3             2              38
D36V2, multiclass
        clus
vv       OR6K3 MUTATED OR6K3 WILD-TYPE
  CLUS_1             1               8
  CLUS_2             1              13
  CLUS_3             1              24
  CLUS_4             0              20
D36V3, binary
                 cls
clus               0  1
  OR6K3 MUTATED    2  1
  OR6K3 WILD-TYPE 20 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6K3 MUTATED      2    1
  OR6K3 WILD-TYPE   20   20
        clus
vv       OR6K3 MUTATED OR6K3 WILD-TYPE
  CLUS_1             2              20
  CLUS_2             1              20
D36V4, multiclass
        clus
vv       OR6K3 MUTATED OR6K3 WILD-TYPE
  CLUS_1             0              15
  CLUS_2             1               6
  CLUS_3             2              19
D36V5, multiclass
        clus
vv       OR6K3 MUTATED OR6K3 WILD-TYPE
  CLUS_1             5              73
  CLUS_2             0              24
  CLUS_3             1              12
D36V6, multiclass
        clus
vv       OR6K3 MUTATED OR6K3 WILD-TYPE
  CLUS_1             1              26
  CLUS_2             4              52
  CLUS_3             1              31

Clustering(37) Variable = TM7SF4 MUTATION ANALYSIS
D37V1, multiclass
        clus
vv       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  CLUS_1              0               20
  CLUS_2              2               53
  CLUS_3              5               35
D37V2, multiclass
        clus
vv       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  CLUS_1              1                8
  CLUS_2              2               12
  CLUS_3              2               23
  CLUS_4              0               20
D37V3, binary
                  cls
clus                0  1
  TM7SF4 MUTATED    2  0
  TM7SF4 WILD-TYPE 20 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED      2    0
  TM7SF4 WILD-TYPE   20   21
        clus
vv       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  CLUS_1              2               20
  CLUS_2              0               21
D37V4, multiclass
[1] "Remove cluster labels:" "TM7SF4 MUTATED"        
clus
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               2               41 
      TCGA-BR-4187       TCGA-BR-4191       TCGA-BR-4201       TCGA-BR-4253 
"TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" 
      TCGA-BR-4255       TCGA-BR-4256       TCGA-BR-4257       TCGA-BR-4267 
"TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" 
      TCGA-BR-4279       TCGA-BR-4280       TCGA-BR-4292       TCGA-BR-4294 
"TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" 
      TCGA-BR-4357       TCGA-BR-4361       TCGA-BR-4362       TCGA-BR-4363 
"TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" 
      TCGA-BR-4366       TCGA-BR-4367       TCGA-BR-4369       TCGA-BR-4370 
"TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" 
      TCGA-BR-4371       TCGA-CG-4301       TCGA-CG-4304       TCGA-CG-4305 
"TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" 
      TCGA-CG-4306       TCGA-CG-4436       TCGA-CG-4438       TCGA-CG-4440 
"TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" 
      TCGA-CG-4442       TCGA-CG-4443       TCGA-CG-4444       TCGA-CG-4449 
"TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" 
      TCGA-CG-4460       TCGA-CG-4462       TCGA-CG-4465       TCGA-CG-4466 
"TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" 
      TCGA-CG-4469       TCGA-CG-4474       TCGA-CG-4475       TCGA-CG-4476 
"TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" "TM7SF4 WILD-TYPE" 
      TCGA-CG-4477 
"TM7SF4 WILD-TYPE" 
D37V5, multiclass
        clus
vv       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  CLUS_1              6               72
  CLUS_2              1               23
  CLUS_3              0               13
D37V6, multiclass
        clus
vv       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  CLUS_1              1               26
  CLUS_2              2               54
  CLUS_3              4               28

Clustering(38) Variable = UPF3A MUTATION ANALYSIS
D38V1, multiclass
        clus
vv       UPF3A MUTATED UPF3A WILD-TYPE
  CLUS_1             2              18
  CLUS_2             1              54
  CLUS_3             3              37
D38V2, multiclass
        clus
vv       UPF3A MUTATED UPF3A WILD-TYPE
  CLUS_1             0               9
  CLUS_2             2              12
  CLUS_3             1              24
  CLUS_4             0              20
D38V3, binary
                 cls
clus               0  1
  UPF3A MUTATED    1  2
  UPF3A WILD-TYPE 21 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UPF3A MUTATED      1    2
  UPF3A WILD-TYPE   21   19
        clus
vv       UPF3A MUTATED UPF3A WILD-TYPE
  CLUS_1             1              21
  CLUS_2             2              19
D38V4, multiclass
        clus
vv       UPF3A MUTATED UPF3A WILD-TYPE
  CLUS_1             2              13
  CLUS_2             0               7
  CLUS_3             1              20
D38V5, multiclass
        clus
vv       UPF3A MUTATED UPF3A WILD-TYPE
  CLUS_1             5              73
  CLUS_2             0              24
  CLUS_3             1              12
D38V6, multiclass
        clus
vv       UPF3A MUTATED UPF3A WILD-TYPE
  CLUS_1             1              26
  CLUS_2             5              51
  CLUS_3             0              32

Clustering(39) Variable = C7ORF63 MUTATION ANALYSIS
D39V1, multiclass
        clus
vv       C7ORF63 MUTATED C7ORF63 WILD-TYPE
  CLUS_1               3                17
  CLUS_2               0                55
  CLUS_3               2                38
D39V2, multiclass
D39V3, binary
                   cls
clus                 0  1
  C7ORF63 MUTATED    2  2
  C7ORF63 WILD-TYPE 20 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF63 MUTATED      2    2
  C7ORF63 WILD-TYPE   20   19
        clus
vv       C7ORF63 MUTATED C7ORF63 WILD-TYPE
  CLUS_1               2                20
  CLUS_2               2                19
D39V4, multiclass
        clus
vv       C7ORF63 MUTATED C7ORF63 WILD-TYPE
  CLUS_1               2                13
  CLUS_2               0                 7
  CLUS_3               2                19
D39V5, multiclass
        clus
vv       C7ORF63 MUTATED C7ORF63 WILD-TYPE
  CLUS_1               5                73
  CLUS_2               0                24
  CLUS_3               0                13
D39V6, multiclass
        clus
vv       C7ORF63 MUTATED C7ORF63 WILD-TYPE
  CLUS_1               0                27
  CLUS_2               4                52
  CLUS_3               1                31

Clustering(40) Variable = KDM4B MUTATION ANALYSIS
D40V1, multiclass
        clus
vv       KDM4B MUTATED KDM4B WILD-TYPE
  CLUS_1             5              15
  CLUS_2             1              54
  CLUS_3             4              36
D40V2, multiclass
        clus
vv       KDM4B MUTATED KDM4B WILD-TYPE
  CLUS_1             0               9
  CLUS_2             3              11
  CLUS_3             1              24
  CLUS_4             0              20
D40V3, binary
                 cls
clus               0  1
  KDM4B MUTATED    4  1
  KDM4B WILD-TYPE 18 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM4B MUTATED      4    1
  KDM4B WILD-TYPE   18   20
        clus
vv       KDM4B MUTATED KDM4B WILD-TYPE
  CLUS_1             4              18
  CLUS_2             1              20
D40V4, multiclass
        clus
vv       KDM4B MUTATED KDM4B WILD-TYPE
  CLUS_1             1              14
  CLUS_2             0               7
  CLUS_3             4              17
D40V5, multiclass
        clus
vv       KDM4B MUTATED KDM4B WILD-TYPE
  CLUS_1             8              70
  CLUS_2             1              23
  CLUS_3             1              12
D40V6, multiclass
        clus
vv       KDM4B MUTATED KDM4B WILD-TYPE
  CLUS_1             1              26
  CLUS_2             6              50
  CLUS_3             3              29

Clustering(41) Variable = KIAA0748 MUTATION ANALYSIS
D41V1, multiclass
        clus
vv       KIAA0748 MUTATED KIAA0748 WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                4                 51
  CLUS_3                1                 39
D41V2, multiclass
        clus
vv       KIAA0748 MUTATED KIAA0748 WILD-TYPE
  CLUS_1                1                  8
  CLUS_2                2                 12
  CLUS_3                1                 24
  CLUS_4                1                 19
D41V3, binary
                    cls
clus                  0  1
  KIAA0748 MUTATED    1  1
  KIAA0748 WILD-TYPE 21 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0748 MUTATED      1    1
  KIAA0748 WILD-TYPE   21   20
        clus
vv       KIAA0748 MUTATED KIAA0748 WILD-TYPE
  CLUS_1                1                 21
  CLUS_2                1                 20
D41V4, multiclass
[1] "Remove cluster labels:" "KIAA0748 MUTATED"      
clus
  KIAA0748 MUTATED KIAA0748 WILD-TYPE 
                 2                 41 
        TCGA-BR-4187         TCGA-BR-4191         TCGA-BR-4201 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-BR-4253         TCGA-BR-4255         TCGA-BR-4256 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-BR-4257         TCGA-BR-4279         TCGA-BR-4280 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-BR-4292         TCGA-BR-4294         TCGA-BR-4357 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-BR-4361         TCGA-BR-4363         TCGA-BR-4366 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-BR-4367         TCGA-BR-4368         TCGA-BR-4369 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-BR-4370         TCGA-BR-4371         TCGA-CG-4301 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4438         TCGA-CG-4440 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-CG-4442         TCGA-CG-4443         TCGA-CG-4444 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4460         TCGA-CG-4462 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4475 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
        TCGA-CG-4476         TCGA-CG-4477 
"KIAA0748 WILD-TYPE" "KIAA0748 WILD-TYPE" 
D41V5, multiclass
        clus
vv       KIAA0748 MUTATED KIAA0748 WILD-TYPE
  CLUS_1                7                 71
  CLUS_2                0                 24
  CLUS_3                0                 13
D41V6, multiclass
        clus
vv       KIAA0748 MUTATED KIAA0748 WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                5                 51
  CLUS_3                1                 31

Clustering(42) Variable = OR8B4 MUTATION ANALYSIS
D42V1, multiclass
        clus
vv       OR8B4 MUTATED OR8B4 WILD-TYPE
  CLUS_1             1              19
  CLUS_2             2              53
  CLUS_3             0              40
D42V2, multiclass
        clus
vv       OR8B4 MUTATED OR8B4 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             3              11
  CLUS_3             0              25
  CLUS_4             0              20
D42V3, binary
                 cls
clus               0  1
  OR8B4 MUTATED    0  0
  OR8B4 WILD-TYPE 22 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8B4 MUTATED      0    0
  OR8B4 WILD-TYPE   22   21
D42V4, multiclass
D42V5, multiclass
        clus
vv       OR8B4 MUTATED OR8B4 WILD-TYPE
  CLUS_1             3              75
  CLUS_2             0              24
  CLUS_3             0              13
D42V6, multiclass
        clus
vv       OR8B4 MUTATED OR8B4 WILD-TYPE
  CLUS_1             1              26
  CLUS_2             2              54
  CLUS_3             0              32

Clustering(43) Variable = POM121L12 MUTATION ANALYSIS
D43V1, multiclass
        clus
vv       POM121L12 MUTATED POM121L12 WILD-TYPE
  CLUS_1                 0                  20
  CLUS_2                 0                  55
  CLUS_3                 7                  33
D43V2, multiclass
        clus
vv       POM121L12 MUTATED POM121L12 WILD-TYPE
  CLUS_1                 1                   8
  CLUS_2                 0                  14
  CLUS_3                 3                  22
  CLUS_4                 0                  20
D43V3, binary
                     cls
clus                   0  1
  POM121L12 MUTATED    2  1
  POM121L12 WILD-TYPE 20 20
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  POM121L12 MUTATED      2    1
  POM121L12 WILD-TYPE   20   20
        clus
vv       POM121L12 MUTATED POM121L12 WILD-TYPE
  CLUS_1                 2                  20
  CLUS_2                 1                  20
D43V4, multiclass
        clus
vv       POM121L12 MUTATED POM121L12 WILD-TYPE
  CLUS_1                 1                  14
  CLUS_2                 1                   6
  CLUS_3                 1                  20
D43V5, multiclass
        clus
vv       POM121L12 MUTATED POM121L12 WILD-TYPE
  CLUS_1                 6                  72
  CLUS_2                 1                  23
  CLUS_3                 0                  13
D43V6, multiclass
        clus
vv       POM121L12 MUTATED POM121L12 WILD-TYPE
  CLUS_1                 0                  27
  CLUS_2                 4                  52
  CLUS_3                 3                  29

Clustering(44) Variable = RASA1 MUTATION ANALYSIS
D44V1, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             4              16
  CLUS_2             4              51
  CLUS_3             1              39
D44V2, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             1              13
  CLUS_3             0              25
  CLUS_4             2              18
D44V3, binary
                 cls
clus               0  1
  RASA1 MUTATED    4  2
  RASA1 WILD-TYPE 18 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED      4    2
  RASA1 WILD-TYPE   18   19
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             4              18
  CLUS_2             2              19
D44V4, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             1              14
  CLUS_2             1               6
  CLUS_3             4              17
D44V5, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             7              71
  CLUS_2             0              24
  CLUS_3             2              11
D44V6, multiclass
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  CLUS_1             3              24
  CLUS_2             5              51
  CLUS_3             1              31

Clustering(45) Variable = SLITRK6 MUTATION ANALYSIS
D45V1, multiclass
        clus
vv       SLITRK6 MUTATED SLITRK6 WILD-TYPE
  CLUS_1               3                17
  CLUS_2               4                51
  CLUS_3               3                37
D45V2, multiclass
        clus
vv       SLITRK6 MUTATED SLITRK6 WILD-TYPE
  CLUS_1               0                 9
  CLUS_2               1                13
  CLUS_3               3                22
  CLUS_4               2                18
D45V3, binary
                   cls
clus                 0  1
  SLITRK6 MUTATED    0  3
  SLITRK6 WILD-TYPE 22 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK6 MUTATED      0    3
  SLITRK6 WILD-TYPE   22   18
        clus
vv       SLITRK6 MUTATED SLITRK6 WILD-TYPE
  CLUS_1               0                22
  CLUS_2               3                18
D45V4, multiclass
        clus
vv       SLITRK6 MUTATED SLITRK6 WILD-TYPE
  CLUS_1               2                13
  CLUS_2               0                 7
  CLUS_3               1                20
D45V5, multiclass
        clus
vv       SLITRK6 MUTATED SLITRK6 WILD-TYPE
  CLUS_1               8                70
  CLUS_2               0                24
  CLUS_3               2                11
D45V6, multiclass
        clus
vv       SLITRK6 MUTATED SLITRK6 WILD-TYPE
  CLUS_1               3                24
  CLUS_2               5                51
  CLUS_3               2                30

Clustering(46) Variable = TP53TG5 MUTATION ANALYSIS
D46V1, multiclass
        clus
vv       TP53TG5 MUTATED TP53TG5 WILD-TYPE
  CLUS_1               2                18
  CLUS_2               2                53
  CLUS_3               0                40
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, binary
                   cls
clus                 0  1
  TP53TG5 MUTATED    1  1
  TP53TG5 WILD-TYPE 21 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53TG5 MUTATED      1    1
  TP53TG5 WILD-TYPE   21   20
        clus
vv       TP53TG5 MUTATED TP53TG5 WILD-TYPE
  CLUS_1               1                21
  CLUS_2               1                20
D46V4, multiclass
[1] "Remove cluster labels:" "TP53TG5 MUTATED"       
clus
  TP53TG5 MUTATED TP53TG5 WILD-TYPE 
                2                41 
       TCGA-BR-4187        TCGA-BR-4191        TCGA-BR-4201        TCGA-BR-4253 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257        TCGA-BR-4267 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362        TCGA-BR-4363 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-4369 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-BR-4370        TCGA-BR-4371        TCGA-CG-4301        TCGA-CG-4304 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4438 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4442        TCGA-CG-4444        TCGA-CG-4449 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" "TP53TG5 WILD-TYPE" 
       TCGA-CG-4477 
"TP53TG5 WILD-TYPE" 
D46V5, multiclass
        clus
vv       TP53TG5 MUTATED TP53TG5 WILD-TYPE
  CLUS_1               3                75
  CLUS_2               1                23
  CLUS_3               0                13
D46V6, multiclass
        clus
vv       TP53TG5 MUTATED TP53TG5 WILD-TYPE
  CLUS_1               0                27
  CLUS_2               3                53
  CLUS_3               1                31

Clustering(47) Variable = LHCGR MUTATION ANALYSIS
D47V1, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             2              18
  CLUS_2             3              52
  CLUS_3             2              38
D47V2, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             1               8
  CLUS_2             1              13
  CLUS_3             1              24
  CLUS_4             1              19
D47V3, binary
                 cls
clus               0  1
  LHCGR MUTATED    2  0
  LHCGR WILD-TYPE 20 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LHCGR MUTATED      2    0
  LHCGR WILD-TYPE   20   21
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             2              20
  CLUS_2             0              21
D47V4, multiclass
[1] "Remove cluster labels:" "LHCGR MUTATED"         
clus
  LHCGR MUTATED LHCGR WILD-TYPE 
              2              41 
     TCGA-BR-4187      TCGA-BR-4191      TCGA-BR-4201      TCGA-BR-4253 
"LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" 
     TCGA-BR-4255      TCGA-BR-4256      TCGA-BR-4257      TCGA-BR-4267 
"LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" 
     TCGA-BR-4279      TCGA-BR-4280      TCGA-BR-4292      TCGA-BR-4294 
"LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" 
     TCGA-BR-4361      TCGA-BR-4362      TCGA-BR-4363      TCGA-BR-4366 
"LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" 
     TCGA-BR-4367      TCGA-BR-4369      TCGA-BR-4370      TCGA-BR-4371 
"LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" 
     TCGA-CG-4301      TCGA-CG-4304      TCGA-CG-4305      TCGA-CG-4306 
"LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" 
     TCGA-CG-4436      TCGA-CG-4438      TCGA-CG-4440      TCGA-CG-4442 
"LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" 
     TCGA-CG-4443      TCGA-CG-4444      TCGA-CG-4449      TCGA-CG-4460 
"LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" 
     TCGA-CG-4462      TCGA-CG-4465      TCGA-CG-4466      TCGA-CG-4469 
"LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" 
     TCGA-CG-4472      TCGA-CG-4474      TCGA-CG-4475      TCGA-CG-4476 
"LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" "LHCGR WILD-TYPE" 
     TCGA-CG-4477 
"LHCGR WILD-TYPE" 
D47V5, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             5              73
  CLUS_2             2              22
  CLUS_3             0              13
D47V6, multiclass
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  CLUS_1             1              26
  CLUS_2             2              54
  CLUS_3             4              28
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"          "MRNASEQ_CNMF" 
                     V4                      V5                      V6 
"MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
