
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/421304/LGG-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/LGG-TP/3537434/LGG-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=LGG-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=LGG-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=232, in cluster file=217, common to both=217
[1]  37 217
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
           165             52 
  IDH1 MUTATED IDH1 WILD-TYPE 
           165             52 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
             9            208 
  IDH2 MUTATED IDH2 WILD-TYPE 
             9            208 
[1] "IL32 MUTATION ANALYSIS"
[1] 3
  IL32 MUTATED IL32 WILD-TYPE 
             6            211 
  IL32 MUTATED IL32 WILD-TYPE 
             6            211 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           113            104 
  TP53 MUTATED TP53 WILD-TYPE 
           113            104 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              14              203 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              14              203 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              19              198 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              19              198 
[1] "ATRX MUTATION ANALYSIS"
[1] 3
  ATRX MUTATED ATRX WILD-TYPE 
            93            124 
  ATRX MUTATED ATRX WILD-TYPE 
            93            124 
[1] "FUBP1 MUTATION ANALYSIS"
[1] 3
  FUBP1 MUTATED FUBP1 WILD-TYPE 
             22             195 
  FUBP1 MUTATED FUBP1 WILD-TYPE 
             22             195 
[1] "CIC MUTATION ANALYSIS"
[1] 3
  CIC MUTATED CIC WILD-TYPE 
           41           176 
  CIC MUTATED CIC WILD-TYPE 
           41           176 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              19              198 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              19              198 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            12            205 
  PTEN MUTATED PTEN WILD-TYPE 
            12            205 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           16           201 
  NF1 MUTATED NF1 WILD-TYPE 
           16           201 
[1] "ZNF844 MUTATION ANALYSIS"
[1] 3
  ZNF844 MUTATED ZNF844 WILD-TYPE 
               6              211 
  ZNF844 MUTATED ZNF844 WILD-TYPE 
               6              211 
[1] "TCF12 MUTATION ANALYSIS"
[1] 3
  TCF12 MUTATED TCF12 WILD-TYPE 
              9             208 
  TCF12 MUTATED TCF12 WILD-TYPE 
              9             208 
[1] "ZBTB20 MUTATION ANALYSIS"
[1] 3
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              10              207 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              10              207 
[1] "TIMD4 MUTATION ANALYSIS"
[1] 3
  TIMD4 MUTATED TIMD4 WILD-TYPE 
              6             211 
  TIMD4 MUTATED TIMD4 WILD-TYPE 
              6             211 
[1] "CREBZF MUTATION ANALYSIS"
[1] 3
  CREBZF MUTATED CREBZF WILD-TYPE 
               4              213 
  CREBZF MUTATED CREBZF WILD-TYPE 
               4              213 
[1] "ZNF57 MUTATION ANALYSIS"
[1] 3
  ZNF57 MUTATED ZNF57 WILD-TYPE 
              6             211 
  ZNF57 MUTATED ZNF57 WILD-TYPE 
              6             211 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              13              204 
  ARID1A MUTATED ARID1A WILD-TYPE 
              13              204 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
            10            207 
  EGFR MUTATED EGFR WILD-TYPE 
            10            207 
[1] "EMG1 MUTATION ANALYSIS"
[1] 3
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            213 
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            213 
[1] "PRAMEF11 MUTATION ANALYSIS"
[1] 3
  PRAMEF11 MUTATED PRAMEF11 WILD-TYPE 
                 6                211 
  PRAMEF11 MUTATED PRAMEF11 WILD-TYPE 
                 6                211 
[1] "PRDM9 MUTATION ANALYSIS"
[1] 3
  PRDM9 MUTATED PRDM9 WILD-TYPE 
              6             211 
  PRDM9 MUTATED PRDM9 WILD-TYPE 
              6             211 
[1] "NOX4 MUTATION ANALYSIS"
[1] 3
  NOX4 MUTATED NOX4 WILD-TYPE 
             5            212 
  NOX4 MUTATED NOX4 WILD-TYPE 
             5            212 
[1] "ANKRD30A MUTATION ANALYSIS"
[1] 3
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 8                209 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 8                209 
[1] "MUC7 MUTATION ANALYSIS"
[1] 3
  MUC7 MUTATED MUC7 WILD-TYPE 
             5            212 
  MUC7 MUTATED MUC7 WILD-TYPE 
             5            212 
[1] "PAX4 MUTATION ANALYSIS"
[1] 3
  PAX4 MUTATED PAX4 WILD-TYPE 
             5            212 
  PAX4 MUTATED PAX4 WILD-TYPE 
             5            212 
[1] "ZNF845 MUTATION ANALYSIS"
[1] 3
  ZNF845 MUTATED ZNF845 WILD-TYPE 
               6              211 
  ZNF845 MUTATED ZNF845 WILD-TYPE 
               6              211 
[1] "C15ORF2 MUTATION ANALYSIS"
[1] 3
  C15ORF2 MUTATED C15ORF2 WILD-TYPE 
                8               209 
  C15ORF2 MUTATED C15ORF2 WILD-TYPE 
                8               209 
[1] "SPDYE5 MUTATION ANALYSIS"
[1] 3
  SPDYE5 MUTATED SPDYE5 WILD-TYPE 
               4              213 
  SPDYE5 MUTATED SPDYE5 WILD-TYPE 
               4              213 
[1] "SCAF1 MUTATION ANALYSIS"
[1] 3
  SCAF1 MUTATED SCAF1 WILD-TYPE 
              4             213 
  SCAF1 MUTATED SCAF1 WILD-TYPE 
              4             213 
[1] "FSTL5 MUTATION ANALYSIS"
[1] 3
  FSTL5 MUTATED FSTL5 WILD-TYPE 
              6             211 
  FSTL5 MUTATED FSTL5 WILD-TYPE 
              6             211 
[1] "C9ORF79 MUTATION ANALYSIS"
[1] 3
  C9ORF79 MUTATED C9ORF79 WILD-TYPE 
                8               209 
  C9ORF79 MUTATED C9ORF79 WILD-TYPE 
                8               209 
[1] "ZCCHC12 MUTATION ANALYSIS"
[1] 3
  ZCCHC12 MUTATED ZCCHC12 WILD-TYPE 
                3               214 
  ZCCHC12 MUTATED ZCCHC12 WILD-TYPE 
                3               214 
[1] "SMARCA4 MUTATION ANALYSIS"
[1] 3
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               13               204 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               13               204 
[1] "MYH4 MUTATION ANALYSIS"
[1] 3
  MYH4 MUTATED MYH4 WILD-TYPE 
             5            212 
  MYH4 MUTATED MYH4 WILD-TYPE 
             5            212 
[1] "TRDN MUTATION ANALYSIS"
[1] 3
  TRDN MUTATED TRDN WILD-TYPE 
             4            213 
  TRDN MUTATED TRDN WILD-TYPE 
             4            213 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 217 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 217 columns, 0 survival variables, and 10 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=6, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = IDH1 MUTATION ANALYSIS
D1V1, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            9              0
  CLUS_2            7              3
  CLUS_3            7              1
D1V2, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            5              2
  CLUS_2            6              0
  CLUS_3            9              1
  CLUS_4            3              1
D1V3, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           78             12
  CLUS_2           17             32
  CLUS_3           69              7
D1V4, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           94              2
  CLUS_2            0             32
  CLUS_3           15             13
  CLUS_4           52              4
D1V5, multiclass
D1V6, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           30              3
  CLUS_2           80             32
  CLUS_3           54             16
D1V7, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           41             14
  CLUS_2           29              4
  CLUS_3           65             17
  CLUS_4           29             17
D1V8, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            5              3
  CLUS_2           78             17
  CLUS_3           81             32
D1V9, multiclass
D1V10, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            2              5
  CLUS_2           82             31
  CLUS_3           80             16

Clustering(2) Variable = IDH2 MUTATION ANALYSIS
D2V1, multiclass
[1] "Remove cluster labels:" "IDH2 MUTATED"          
clus
  IDH2 MUTATED IDH2 WILD-TYPE 
             2             25 
    TCGA-CS-4942     TCGA-CS-4943     TCGA-CS-4944     TCGA-CS-5390 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-CS-5394     TCGA-CS-5395     TCGA-CS-5396     TCGA-DB-5270 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DB-5273     TCGA-DB-5274     TCGA-DB-5275     TCGA-DB-5276 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DB-5277     TCGA-DB-5278     TCGA-DB-5280     TCGA-DB-5281 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DH-5140     TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-E1-5302     TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-E1-5322 
"IDH2 WILD-TYPE" 
D2V2, multiclass
[1] "Remove cluster labels:" "IDH2 MUTATED"          
clus
  IDH2 MUTATED IDH2 WILD-TYPE 
             2             25 
    TCGA-CS-4942     TCGA-CS-4943     TCGA-CS-4944     TCGA-CS-5390 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-CS-5394     TCGA-CS-5395     TCGA-CS-5396     TCGA-DB-5270 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DB-5273     TCGA-DB-5274     TCGA-DB-5275     TCGA-DB-5276 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DB-5277     TCGA-DB-5278     TCGA-DB-5280     TCGA-DB-5281 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DH-5140     TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-E1-5302     TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-E1-5322 
"IDH2 WILD-TYPE" 
D2V3, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            3             87
  CLUS_2            0             49
  CLUS_3            6             70
D2V4, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            2             94
  CLUS_2            0             32
  CLUS_3            3             25
  CLUS_4            4             52
D2V5, multiclass
D2V6, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            3             30
  CLUS_2            0            112
  CLUS_3            6             64
D2V7, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            0             55
  CLUS_2            3             30
  CLUS_3            6             76
  CLUS_4            0             46
D2V8, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            6             89
  CLUS_3            3            110
D2V9, multiclass
D2V10, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            0              7
  CLUS_2            3            110
  CLUS_3            6             90

Clustering(3) Variable = IL32 MUTATION ANALYSIS
D3V1, multiclass
[1] "Remove cluster labels:" "IL32 MUTATED"          
clus
  IL32 MUTATED IL32 WILD-TYPE 
             1             26 
    TCGA-CS-4942     TCGA-CS-4943     TCGA-CS-4944     TCGA-CS-5390 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-CS-5395     TCGA-CS-5396     TCGA-DB-5270     TCGA-DB-5273 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DB-5274     TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DB-5278     TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DH-5141     TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-E1-5302     TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-E1-5318     TCGA-E1-5322 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" 
D3V2, multiclass
[1] "Remove cluster labels:" "IL32 MUTATED"          
clus
  IL32 MUTATED IL32 WILD-TYPE 
             1             26 
    TCGA-CS-4942     TCGA-CS-4943     TCGA-CS-4944     TCGA-CS-5390 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-CS-5395     TCGA-CS-5396     TCGA-DB-5270     TCGA-DB-5273 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DB-5274     TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DB-5278     TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DH-5141     TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-E1-5302     TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-E1-5318     TCGA-E1-5322 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" 
D3V3, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            0             90
  CLUS_2            2             47
  CLUS_3            4             72
D3V4, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            0             96
  CLUS_2            2             30
  CLUS_3            1             27
  CLUS_4            3             53
D3V5, multiclass
D3V6, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            2             31
  CLUS_2            2            110
  CLUS_3            2             68
D3V7, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            1             54
  CLUS_2            2             31
  CLUS_3            3             79
  CLUS_4            0             46
D3V8, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            1              7
  CLUS_2            2             93
  CLUS_3            3            110
D3V9, multiclass
D3V10, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            0              7
  CLUS_2            2            111
  CLUS_3            4             92

Clustering(4) Variable = TP53 MUTATION ANALYSIS
D4V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8              1
  CLUS_2            4              6
  CLUS_3            5              3
D4V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              6
  CLUS_2            4              2
  CLUS_3            8              2
  CLUS_4            4              0
D4V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           80             10
  CLUS_2           22             27
  CLUS_3           11             65
D4V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           95              1
  CLUS_2            6             26
  CLUS_3            8             20
  CLUS_4            3             53
D4V5, multiclass
D4V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             31
  CLUS_2           80             32
  CLUS_3           30             40
D4V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           35             20
  CLUS_2           12             21
  CLUS_3           33             49
  CLUS_4           32             14
D4V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              5
  CLUS_2           40             55
  CLUS_3           69             44
D4V9, multiclass
D4V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              6
  CLUS_2           72             41
  CLUS_3           39             57

Clustering(5) Variable = PIK3R1 MUTATION ANALYSIS
D5V1, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              2                7
  CLUS_2              1                9
  CLUS_3              0                8
D5V2, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              1                6
  CLUS_2              0                6
  CLUS_3              2                8
  CLUS_4              0                4
D5V3, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              1               89
  CLUS_2              3               46
  CLUS_3             10               66
D5V4, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              2               94
  CLUS_2              2               30
  CLUS_3              1               27
  CLUS_4              7               49
D5V5, multiclass
D5V6, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              3               30
  CLUS_2              5              107
  CLUS_3              5               65
D5V7, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              4               51
  CLUS_2              3               30
  CLUS_3              5               77
  CLUS_4              2               44
D5V8, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              0                8
  CLUS_2              6               89
  CLUS_3              8              105
D5V9, multiclass
D5V10, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              0                7
  CLUS_2              8              105
  CLUS_3              6               90

Clustering(6) Variable = PIK3CA MUTATION ANALYSIS
D6V1, multiclass
D6V2, multiclass
D6V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1               89
  CLUS_2              5               44
  CLUS_3             13               63
D6V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1               95
  CLUS_2              5               27
  CLUS_3              3               25
  CLUS_4             10               46
D6V5, multiclass
D6V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5               28
  CLUS_2              8              104
  CLUS_3              6               64
D6V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2               53
  CLUS_2              4               29
  CLUS_3              8               74
  CLUS_4              5               41
D6V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2                6
  CLUS_2              8               87
  CLUS_3              9              104
D6V9, multiclass
D6V10, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1                6
  CLUS_2              9              104
  CLUS_3              9               87

Clustering(7) Variable = ATRX MUTATION ANALYSIS
D7V1, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            8              1
  CLUS_2            3              7
  CLUS_3            3              5
D7V2, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            1              6
  CLUS_2            3              3
  CLUS_3            8              2
  CLUS_4            2              2
D7V3, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           66             24
  CLUS_2           17             32
  CLUS_3           10             66
D7V4, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           80             16
  CLUS_2            4             28
  CLUS_3            6             22
  CLUS_4            2             54
D7V5, multiclass
D7V6, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            1             32
  CLUS_2           64             48
  CLUS_3           27             43
D7V7, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           25             30
  CLUS_2           10             23
  CLUS_3           27             55
  CLUS_4           30             16
D7V8, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            2              6
  CLUS_2           33             62
  CLUS_3           57             56
D7V9, multiclass
D7V10, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            1              6
  CLUS_2           59             54
  CLUS_3           32             64

Clustering(8) Variable = FUBP1 MUTATION ANALYSIS
D8V1, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             4               6
  CLUS_3             0               8
D8V2, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             4               3
  CLUS_2             0               6
  CLUS_3             0              10
  CLUS_4             0               4
D8V3, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0              90
  CLUS_2             1              48
  CLUS_3            21              55
D8V4, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0              96
  CLUS_2             1              31
  CLUS_3             2              26
  CLUS_4            16              40
D8V5, multiclass
D8V6, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1            13              20
  CLUS_2             3             109
  CLUS_3             6              64
D8V7, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             5              50
  CLUS_2             8              25
  CLUS_3             8              74
  CLUS_4             1              45
D8V8, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             1               7
  CLUS_2            13              82
  CLUS_3             8             105
D8V9, multiclass
D8V10, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             1               6
  CLUS_2             8             105
  CLUS_3            13              83

Clustering(9) Variable = CIC MUTATION ANALYSIS
D9V1, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0             9
  CLUS_2           5             5
  CLUS_3           2             6
D9V2, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           5             2
  CLUS_2           2             4
  CLUS_3           0            10
  CLUS_4           0             4
D9V3, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           1            89
  CLUS_2           1            48
  CLUS_3          39            37
D9V4, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0            96
  CLUS_2           1            31
  CLUS_3           3            25
  CLUS_4          36            20
D9V5, multiclass
D9V6, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1          22            11
  CLUS_2           3           109
  CLUS_3          16            54
D9V7, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           6            49
  CLUS_2          16            17
  CLUS_3          18            64
  CLUS_4           1            45
D9V8, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0             8
  CLUS_2          27            68
  CLUS_3          14            99
D9V9, multiclass
D9V10, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0             7
  CLUS_2          13           100
  CLUS_3          28            68

Clustering(10) Variable = NOTCH1 MUTATION ANALYSIS
D10V1, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              2                8
  CLUS_3              1                7
D10V2, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              2                5
  CLUS_2              1                5
  CLUS_3              0               10
  CLUS_4              0                4
D10V3, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               89
  CLUS_2              2               47
  CLUS_3             16               60
D10V4, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              2               94
  CLUS_2              1               31
  CLUS_3              0               28
  CLUS_4             15               41
D10V5, multiclass
D10V6, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              9               24
  CLUS_2              2              110
  CLUS_3              8               62
D10V7, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               54
  CLUS_2              7               26
  CLUS_3             10               72
  CLUS_4              1               45
D10V8, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              0                8
  CLUS_2             16               79
  CLUS_3              3              110
D10V9, multiclass
D10V10, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              0                7
  CLUS_2              2              111
  CLUS_3             17               79

Clustering(11) Variable = PTEN MUTATION ANALYSIS
D11V1, multiclass
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             1             26 
    TCGA-CS-4942     TCGA-CS-4943     TCGA-CS-4944     TCGA-CS-5390 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CS-5394     TCGA-CS-5396     TCGA-DB-5270     TCGA-DB-5273 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DB-5274     TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DB-5278     TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DH-5141     TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-E1-5302     TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-E1-5318     TCGA-E1-5322 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" 
D11V2, multiclass
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             1             26 
    TCGA-CS-4942     TCGA-CS-4943     TCGA-CS-4944     TCGA-CS-5390 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CS-5394     TCGA-CS-5396     TCGA-DB-5270     TCGA-DB-5273 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DB-5274     TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DB-5278     TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DH-5141     TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-E1-5302     TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-E1-5318     TCGA-E1-5322 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" 
D11V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             90
  CLUS_2           12             37
  CLUS_3            0             76
D11V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             96
  CLUS_2           11             21
  CLUS_3            0             28
  CLUS_4            0             56
D11V5, multiclass
D11V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             33
  CLUS_2           12            100
  CLUS_3            0             70
D11V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            8             47
  CLUS_2            0             33
  CLUS_3            0             82
  CLUS_4            4             42
D11V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0              8
  CLUS_2            1             94
  CLUS_3           11            102
D11V9, multiclass
D11V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            2              5
  CLUS_2            9            104
  CLUS_3            1             95

Clustering(12) Variable = NF1 MUTATION ANALYSIS
D12V1, multiclass
[1] "Remove cluster labels:" "NF1 MUTATED"           
clus
  NF1 MUTATED NF1 WILD-TYPE 
            1            26 
   TCGA-CS-4942    TCGA-CS-4943    TCGA-CS-4944    TCGA-CS-5390    TCGA-CS-5394 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-CS-5395    TCGA-CS-5396    TCGA-DB-5270    TCGA-DB-5273    TCGA-DB-5274 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-DB-5275    TCGA-DB-5276    TCGA-DB-5277    TCGA-DB-5278    TCGA-DB-5280 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-DB-5281    TCGA-DH-5141    TCGA-DH-5142    TCGA-DH-5143    TCGA-DH-5144 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-E1-5302    TCGA-E1-5303    TCGA-E1-5304    TCGA-E1-5311    TCGA-E1-5318 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-E1-5322 
"NF1 WILD-TYPE" 
D12V2, multiclass
[1] "Remove cluster labels:" "NF1 MUTATED"           
clus
  NF1 MUTATED NF1 WILD-TYPE 
            1            26 
   TCGA-CS-4942    TCGA-CS-4943    TCGA-CS-4944    TCGA-CS-5390    TCGA-CS-5394 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-CS-5395    TCGA-CS-5396    TCGA-DB-5270    TCGA-DB-5273    TCGA-DB-5274 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-DB-5275    TCGA-DB-5276    TCGA-DB-5277    TCGA-DB-5278    TCGA-DB-5280 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-DB-5281    TCGA-DH-5141    TCGA-DH-5142    TCGA-DH-5143    TCGA-DH-5144 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-E1-5302    TCGA-E1-5303    TCGA-E1-5304    TCGA-E1-5311    TCGA-E1-5318 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-E1-5322 
"NF1 WILD-TYPE" 
D12V3, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            86
  CLUS_2           8            41
  CLUS_3           4            72
D12V4, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            95
  CLUS_2           8            24
  CLUS_3           3            25
  CLUS_4           0            56
D12V5, multiclass
D12V6, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           2            31
  CLUS_2          10           102
  CLUS_3           4            66
D12V7, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            51
  CLUS_2           2            31
  CLUS_3           4            78
  CLUS_4           6            40
D12V8, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1             7
  CLUS_2           6            89
  CLUS_3           9           104
D12V9, multiclass
D12V10, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1             6
  CLUS_2          11           102
  CLUS_3           4            92

Clustering(13) Variable = ZNF844 MUTATION ANALYSIS
D13V1, multiclass
D13V2, multiclass
D13V3, multiclass
        clus
vv       ZNF844 MUTATED ZNF844 WILD-TYPE
  CLUS_1              3               87
  CLUS_2              1               48
  CLUS_3              2               74
D13V4, multiclass
        clus
vv       ZNF844 MUTATED ZNF844 WILD-TYPE
  CLUS_1              3               93
  CLUS_2              2               30
  CLUS_3              0               28
  CLUS_4              1               55
D13V5, multiclass
D13V6, multiclass
        clus
vv       ZNF844 MUTATED ZNF844 WILD-TYPE
  CLUS_1              0               33
  CLUS_2              3              109
  CLUS_3              3               67
D13V7, multiclass
        clus
vv       ZNF844 MUTATED ZNF844 WILD-TYPE
  CLUS_1              0               55
  CLUS_2              0               33
  CLUS_3              3               79
  CLUS_4              3               43
D13V8, multiclass
        clus
vv       ZNF844 MUTATED ZNF844 WILD-TYPE
  CLUS_1              0                8
  CLUS_2              3               92
  CLUS_3              3              110
D13V9, multiclass
D13V10, multiclass
        clus
vv       ZNF844 MUTATED ZNF844 WILD-TYPE
  CLUS_1              0                7
  CLUS_2              4              109
  CLUS_3              2               94

Clustering(14) Variable = TCF12 MUTATION ANALYSIS
D14V1, multiclass
[1] "Remove cluster labels:" "TCF12 MUTATED"         
clus
  TCF12 MUTATED TCF12 WILD-TYPE 
              1              26 
     TCGA-CS-4942      TCGA-CS-4943      TCGA-CS-4944      TCGA-CS-5390 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-CS-5394      TCGA-CS-5395      TCGA-CS-5396      TCGA-DB-5273 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-DB-5274      TCGA-DB-5275      TCGA-DB-5276      TCGA-DB-5277 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-DB-5278      TCGA-DB-5280      TCGA-DB-5281      TCGA-DH-5140 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-DH-5141      TCGA-DH-5142      TCGA-DH-5143      TCGA-DH-5144 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304      TCGA-E1-5311 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-E1-5318      TCGA-E1-5322 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
D14V2, multiclass
[1] "Remove cluster labels:" "TCF12 MUTATED"         
clus
  TCF12 MUTATED TCF12 WILD-TYPE 
              1              26 
     TCGA-CS-4942      TCGA-CS-4943      TCGA-CS-4944      TCGA-CS-5390 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-CS-5394      TCGA-CS-5395      TCGA-CS-5396      TCGA-DB-5273 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-DB-5274      TCGA-DB-5275      TCGA-DB-5276      TCGA-DB-5277 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-DB-5278      TCGA-DB-5280      TCGA-DB-5281      TCGA-DH-5140 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-DH-5141      TCGA-DH-5142      TCGA-DH-5143      TCGA-DH-5144 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304      TCGA-E1-5311 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-E1-5318      TCGA-E1-5322 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
D14V3, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             3              87
  CLUS_2             2              47
  CLUS_3             4              72
D14V4, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             3              93
  CLUS_2             1              31
  CLUS_3             1              27
  CLUS_4             4              52
D14V5, multiclass
D14V6, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             3              30
  CLUS_2             3             109
  CLUS_3             3              67
D14V7, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             3              52
  CLUS_2             2              31
  CLUS_3             4              78
  CLUS_4             0              46
D14V8, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             5              90
  CLUS_3             4             109
D14V9, multiclass
D14V10, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             0               7
  CLUS_2             3             110
  CLUS_3             6              90

Clustering(15) Variable = ZBTB20 MUTATION ANALYSIS
D15V1, multiclass
D15V2, multiclass
D15V3, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              2               88
  CLUS_2              2               47
  CLUS_3              5               71
D15V4, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              2               94
  CLUS_2              2               30
  CLUS_3              1               27
  CLUS_4              4               52
D15V5, multiclass
D15V6, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              1               32
  CLUS_2              5              107
  CLUS_3              4               66
D15V7, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              2               53
  CLUS_2              1               32
  CLUS_3              4               78
  CLUS_4              3               43
D15V8, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              1                7
  CLUS_2              4               91
  CLUS_3              5              108
D15V9, multiclass
D15V10, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              0                7
  CLUS_2              5              108
  CLUS_3              5               91

Clustering(16) Variable = TIMD4 MUTATION ANALYSIS
D16V1, multiclass
D16V2, multiclass
D16V3, multiclass
        clus
vv       TIMD4 MUTATED TIMD4 WILD-TYPE
  CLUS_1             4              86
  CLUS_2             1              48
  CLUS_3             1              75
D16V4, multiclass
        clus
vv       TIMD4 MUTATED TIMD4 WILD-TYPE
  CLUS_1             3              93
  CLUS_2             1              31
  CLUS_3             1              27
  CLUS_4             1              55
D16V5, multiclass
D16V6, multiclass
        clus
vv       TIMD4 MUTATED TIMD4 WILD-TYPE
  CLUS_1             0              33
  CLUS_2             4             108
  CLUS_3             2              68
D16V7, multiclass
        clus
vv       TIMD4 MUTATED TIMD4 WILD-TYPE
  CLUS_1             3              52
  CLUS_2             1              32
  CLUS_3             1              81
  CLUS_4             1              45
D16V8, multiclass
        clus
vv       TIMD4 MUTATED TIMD4 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             2              93
  CLUS_3             4             109
D16V9, multiclass
D16V10, multiclass
        clus
vv       TIMD4 MUTATED TIMD4 WILD-TYPE
  CLUS_1             1               6
  CLUS_2             3             110
  CLUS_3             2              94

Clustering(17) Variable = CREBZF MUTATION ANALYSIS
D17V1, multiclass
D17V2, multiclass
D17V3, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               90
  CLUS_2              1               48
  CLUS_3              3               73
D17V4, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               96
  CLUS_2              0               32
  CLUS_3              1               27
  CLUS_4              3               53
D17V5, multiclass
D17V6, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              1               32
  CLUS_2              0              112
  CLUS_3              3               67
D17V7, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               55
  CLUS_2              1               32
  CLUS_3              3               79
  CLUS_4              0               46
D17V8, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0                8
  CLUS_2              4               91
  CLUS_3              0              113
D17V9, multiclass
D17V10, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0                7
  CLUS_2              0              113
  CLUS_3              4               92

Clustering(18) Variable = ZNF57 MUTATION ANALYSIS
D18V1, multiclass
D18V2, multiclass
D18V3, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             4              86
  CLUS_2             2              47
  CLUS_3             0              76
D18V4, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             4              92
  CLUS_2             2              30
  CLUS_3             0              28
  CLUS_4             0              56
D18V5, multiclass
D18V6, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             0              33
  CLUS_2             6             106
  CLUS_3             0              70
D18V7, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             4              51
  CLUS_2             0              33
  CLUS_3             0              82
  CLUS_4             2              44
D18V8, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             1              94
  CLUS_3             5             108
D18V9, multiclass
D18V10, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             0               7
  CLUS_2             5             108
  CLUS_3             1              95

Clustering(19) Variable = ARID1A MUTATION ANALYSIS
D19V1, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               1               26 
      TCGA-CS-4942       TCGA-CS-4943       TCGA-CS-4944       TCGA-CS-5390 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-CS-5394       TCGA-CS-5395       TCGA-CS-5396       TCGA-DB-5270 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DB-5273       TCGA-DB-5274       TCGA-DB-5276       TCGA-DB-5277 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DB-5278       TCGA-DB-5280       TCGA-DB-5281       TCGA-DH-5140 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DH-5141       TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-E1-5302       TCGA-E1-5303       TCGA-E1-5304       TCGA-E1-5311 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-E1-5318       TCGA-E1-5322 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
D19V2, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               1               26 
      TCGA-CS-4942       TCGA-CS-4943       TCGA-CS-4944       TCGA-CS-5390 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-CS-5394       TCGA-CS-5395       TCGA-CS-5396       TCGA-DB-5270 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DB-5273       TCGA-DB-5274       TCGA-DB-5276       TCGA-DB-5277 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DB-5278       TCGA-DB-5280       TCGA-DB-5281       TCGA-DH-5140 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DH-5141       TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-E1-5302       TCGA-E1-5303       TCGA-E1-5304       TCGA-E1-5311 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-E1-5318       TCGA-E1-5322 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
D19V3, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              6               84
  CLUS_2              2               47
  CLUS_3              4               72
D19V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              6               90
  CLUS_2              2               30
  CLUS_3              0               28
  CLUS_4              5               51
D19V5, multiclass
D19V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               30
  CLUS_2              4              108
  CLUS_3              5               65
D19V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               54
  CLUS_2              3               30
  CLUS_3              5               77
  CLUS_4              4               42
D19V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0                8
  CLUS_2              7               88
  CLUS_3              6              107
D19V9, multiclass
D19V10, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              0                7
  CLUS_2              6              107
  CLUS_3              7               89

Clustering(20) Variable = EGFR MUTATION ANALYSIS
D20V1, multiclass
D20V2, multiclass
D20V3, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            1             89
  CLUS_2            9             40
  CLUS_3            0             76
D20V4, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0             96
  CLUS_2            8             24
  CLUS_3            2             26
  CLUS_4            0             56
D20V5, multiclass
D20V6, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0             33
  CLUS_2            7            105
  CLUS_3            3             67
D20V7, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            2             53
  CLUS_2            0             33
  CLUS_3            3             79
  CLUS_4            5             41
D20V8, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0              8
  CLUS_2            4             91
  CLUS_3            6            107
D20V9, multiclass
D20V10, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0              7
  CLUS_2            6            107
  CLUS_3            4             92

Clustering(21) Variable = EMG1 MUTATION ANALYSIS
D21V1, multiclass
D21V2, multiclass
D21V3, multiclass
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  CLUS_1            2             88
  CLUS_2            0             49
  CLUS_3            2             74
D21V4, multiclass
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  CLUS_1            2             94
  CLUS_2            0             32
  CLUS_3            1             27
  CLUS_4            1             55
D21V5, multiclass
D21V6, multiclass
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  CLUS_1            1             32
  CLUS_2            2            110
  CLUS_3            1             69
D21V7, multiclass
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  CLUS_1            3             52
  CLUS_2            0             33
  CLUS_3            1             81
  CLUS_4            0             46
D21V8, multiclass
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            1             94
  CLUS_3            3            110
D21V9, multiclass
D21V10, multiclass
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  CLUS_1            0              7
  CLUS_2            3            110
  CLUS_3            1             95

Clustering(22) Variable = PRAMEF11 MUTATION ANALYSIS
D22V1, multiclass
D22V2, multiclass
D22V3, multiclass
        clus
vv       PRAMEF11 MUTATED PRAMEF11 WILD-TYPE
  CLUS_1                3                 87
  CLUS_2                1                 48
  CLUS_3                2                 74
D22V4, multiclass
        clus
vv       PRAMEF11 MUTATED PRAMEF11 WILD-TYPE
  CLUS_1                2                 94
  CLUS_2                1                 31
  CLUS_3                2                 26
  CLUS_4                1                 55
D22V5, multiclass
D22V6, multiclass
        clus
vv       PRAMEF11 MUTATED PRAMEF11 WILD-TYPE
  CLUS_1                0                 33
  CLUS_2                2                110
  CLUS_3                4                 66
D22V7, multiclass
        clus
vv       PRAMEF11 MUTATED PRAMEF11 WILD-TYPE
  CLUS_1                0                 55
  CLUS_2                0                 33
  CLUS_3                4                 78
  CLUS_4                2                 44
D22V8, multiclass
        clus
vv       PRAMEF11 MUTATED PRAMEF11 WILD-TYPE
  CLUS_1                0                  8
  CLUS_2                6                 89
  CLUS_3                0                113
D22V9, multiclass
D22V10, multiclass
        clus
vv       PRAMEF11 MUTATED PRAMEF11 WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                0                113
  CLUS_3                6                 90

Clustering(23) Variable = PRDM9 MUTATION ANALYSIS
D23V1, multiclass
D23V2, multiclass
D23V3, multiclass
        clus
vv       PRDM9 MUTATED PRDM9 WILD-TYPE
  CLUS_1             3              87
  CLUS_2             2              47
  CLUS_3             1              75
D23V4, multiclass
        clus
vv       PRDM9 MUTATED PRDM9 WILD-TYPE
  CLUS_1             4              92
  CLUS_2             2              30
  CLUS_3             0              28
  CLUS_4             0              56
D23V5, multiclass
D23V6, multiclass
        clus
vv       PRDM9 MUTATED PRDM9 WILD-TYPE
  CLUS_1             0              33
  CLUS_2             4             108
  CLUS_3             2              68
D23V7, multiclass
        clus
vv       PRDM9 MUTATED PRDM9 WILD-TYPE
  CLUS_1             1              54
  CLUS_2             0              33
  CLUS_3             2              80
  CLUS_4             3              43
D23V8, multiclass
        clus
vv       PRDM9 MUTATED PRDM9 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             3              92
  CLUS_3             3             110
D23V9, multiclass
D23V10, multiclass
        clus
vv       PRDM9 MUTATED PRDM9 WILD-TYPE
  CLUS_1             0               7
  CLUS_2             3             110
  CLUS_3             3              93

Clustering(24) Variable = NOX4 MUTATION ANALYSIS
D24V1, multiclass
D24V2, multiclass
D24V3, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            0             90
  CLUS_2            2             47
  CLUS_3            3             73
D24V4, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            2             94
  CLUS_2            1             31
  CLUS_3            0             28
  CLUS_4            2             54
D24V5, multiclass
D24V6, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            1             32
  CLUS_2            1            111
  CLUS_3            3             67
D24V7, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            1             54
  CLUS_2            0             33
  CLUS_3            3             79
  CLUS_4            1             45
D24V8, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            4             91
  CLUS_3            1            112
D24V9, multiclass
D24V10, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            0              7
  CLUS_2            1            112
  CLUS_3            4             92

Clustering(25) Variable = ANKRD30A MUTATION ANALYSIS
D25V1, multiclass
D25V2, multiclass
D25V3, multiclass
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  CLUS_1                2                 88
  CLUS_2                2                 47
  CLUS_3                4                 72
D25V4, multiclass
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  CLUS_1                2                 94
  CLUS_2                1                 31
  CLUS_3                3                 25
  CLUS_4                2                 54
D25V5, multiclass
D25V6, multiclass
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  CLUS_1                1                 32
  CLUS_2                4                108
  CLUS_3                3                 67
D25V7, multiclass
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  CLUS_1                1                 54
  CLUS_2                0                 33
  CLUS_3                5                 77
  CLUS_4                2                 44
D25V8, multiclass
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  CLUS_1                1                  7
  CLUS_2                4                 91
  CLUS_3                3                110
D25V9, multiclass
D25V10, multiclass
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                3                110
  CLUS_3                4                 92

Clustering(26) Variable = MUC7 MUTATION ANALYSIS
D26V1, multiclass
D26V2, multiclass
D26V3, multiclass
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  CLUS_1            3             87
  CLUS_2            2             47
  CLUS_3            0             76
D26V4, multiclass
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  CLUS_1            3             93
  CLUS_2            2             30
  CLUS_3            0             28
  CLUS_4            0             56
D26V5, multiclass
D26V6, multiclass
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  CLUS_1            0             33
  CLUS_2            4            108
  CLUS_3            1             69
D26V7, multiclass
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  CLUS_1            1             54
  CLUS_2            0             33
  CLUS_3            2             80
  CLUS_4            2             44
D26V8, multiclass
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            3             92
  CLUS_3            2            111
D26V9, multiclass
D26V10, multiclass
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  CLUS_1            0              7
  CLUS_2            3            110
  CLUS_3            2             94

Clustering(27) Variable = PAX4 MUTATION ANALYSIS
D27V1, multiclass
[1] "Remove cluster labels:" "PAX4 MUTATED"          
clus
  PAX4 MUTATED PAX4 WILD-TYPE 
             1             26 
    TCGA-CS-4942     TCGA-CS-4943     TCGA-CS-4944     TCGA-CS-5390 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-CS-5395     TCGA-CS-5396     TCGA-DB-5270     TCGA-DB-5273 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-DB-5274     TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-DB-5278     TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-DH-5141     TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-E1-5302     TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-E1-5318     TCGA-E1-5322 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
D27V2, multiclass
[1] "Remove cluster labels:" "PAX4 MUTATED"          
clus
  PAX4 MUTATED PAX4 WILD-TYPE 
             1             26 
    TCGA-CS-4942     TCGA-CS-4943     TCGA-CS-4944     TCGA-CS-5390 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-CS-5395     TCGA-CS-5396     TCGA-DB-5270     TCGA-DB-5273 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-DB-5274     TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-DB-5278     TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-DH-5141     TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-E1-5302     TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
    TCGA-E1-5318     TCGA-E1-5322 
"PAX4 WILD-TYPE" "PAX4 WILD-TYPE" 
D27V3, multiclass
        clus
vv       PAX4 MUTATED PAX4 WILD-TYPE
  CLUS_1            1             89
  CLUS_2            2             47
  CLUS_3            2             74
D27V4, multiclass
        clus
vv       PAX4 MUTATED PAX4 WILD-TYPE
  CLUS_1            2             94
  CLUS_2            1             31
  CLUS_3            0             28
  CLUS_4            2             54
D27V5, multiclass
D27V6, multiclass
        clus
vv       PAX4 MUTATED PAX4 WILD-TYPE
  CLUS_1            1             32
  CLUS_2            2            110
  CLUS_3            2             68
D27V7, multiclass
        clus
vv       PAX4 MUTATED PAX4 WILD-TYPE
  CLUS_1            0             55
  CLUS_2            1             32
  CLUS_3            2             80
  CLUS_4            2             44
D27V8, multiclass
        clus
vv       PAX4 MUTATED PAX4 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            3             92
  CLUS_3            2            111
D27V9, multiclass
D27V10, multiclass
        clus
vv       PAX4 MUTATED PAX4 WILD-TYPE
  CLUS_1            0              7
  CLUS_2            2            111
  CLUS_3            3             93

Clustering(28) Variable = ZNF845 MUTATION ANALYSIS
D28V1, multiclass
[1] "Remove cluster labels:" "ZNF845 MUTATED"        
clus
  ZNF845 MUTATED ZNF845 WILD-TYPE 
               1               26 
      TCGA-CS-4942       TCGA-CS-4943       TCGA-CS-4944       TCGA-CS-5390 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-CS-5394       TCGA-CS-5395       TCGA-CS-5396       TCGA-DB-5270 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-DB-5273       TCGA-DB-5274       TCGA-DB-5275       TCGA-DB-5276 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-DB-5277       TCGA-DB-5278       TCGA-DB-5280       TCGA-DH-5140 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-DH-5141       TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-E1-5302       TCGA-E1-5303       TCGA-E1-5304       TCGA-E1-5311 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-E1-5318       TCGA-E1-5322 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
D28V2, multiclass
[1] "Remove cluster labels:" "ZNF845 MUTATED"        
clus
  ZNF845 MUTATED ZNF845 WILD-TYPE 
               1               26 
      TCGA-CS-4942       TCGA-CS-4943       TCGA-CS-4944       TCGA-CS-5390 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-CS-5394       TCGA-CS-5395       TCGA-CS-5396       TCGA-DB-5270 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-DB-5273       TCGA-DB-5274       TCGA-DB-5275       TCGA-DB-5276 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-DB-5277       TCGA-DB-5278       TCGA-DB-5280       TCGA-DH-5140 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-DH-5141       TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-E1-5302       TCGA-E1-5303       TCGA-E1-5304       TCGA-E1-5311 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-E1-5318       TCGA-E1-5322 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
D28V3, multiclass
        clus
vv       ZNF845 MUTATED ZNF845 WILD-TYPE
  CLUS_1              2               88
  CLUS_2              3               46
  CLUS_3              1               75
D28V4, multiclass
        clus
vv       ZNF845 MUTATED ZNF845 WILD-TYPE
  CLUS_1              4               92
  CLUS_2              1               31
  CLUS_3              0               28
  CLUS_4              1               55
D28V5, multiclass
D28V6, multiclass
        clus
vv       ZNF845 MUTATED ZNF845 WILD-TYPE
  CLUS_1              0               33
  CLUS_2              3              109
  CLUS_3              3               67
D28V7, multiclass
        clus
vv       ZNF845 MUTATED ZNF845 WILD-TYPE
  CLUS_1              2               53
  CLUS_2              0               33
  CLUS_3              3               79
  CLUS_4              1               45
D28V8, multiclass
        clus
vv       ZNF845 MUTATED ZNF845 WILD-TYPE
  CLUS_1              0                8
  CLUS_2              4               91
  CLUS_3              2              111
D28V9, multiclass
D28V10, multiclass
        clus
vv       ZNF845 MUTATED ZNF845 WILD-TYPE
  CLUS_1              0                7
  CLUS_2              2              111
  CLUS_3              4               92

Clustering(29) Variable = C15ORF2 MUTATION ANALYSIS
D29V1, multiclass
[1] "Remove cluster labels:" "C15ORF2 MUTATED"       
clus
  C15ORF2 MUTATED C15ORF2 WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5396        TCGA-DB-5270        TCGA-DB-5273 
"C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" 
       TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" 
D29V2, multiclass
[1] "Remove cluster labels:" "C15ORF2 MUTATED"       
clus
  C15ORF2 MUTATED C15ORF2 WILD-TYPE 
                1                26 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5396        TCGA-DB-5270        TCGA-DB-5273 
"C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" 
       TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" 
       TCGA-E1-5302        TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311 
"C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" 
       TCGA-E1-5318        TCGA-E1-5322 
"C15ORF2 WILD-TYPE" "C15ORF2 WILD-TYPE" 
D29V3, multiclass
        clus
vv       C15ORF2 MUTATED C15ORF2 WILD-TYPE
  CLUS_1               2                88
  CLUS_2               4                45
  CLUS_3               2                74
D29V4, multiclass
        clus
vv       C15ORF2 MUTATED C15ORF2 WILD-TYPE
  CLUS_1               3                93
  CLUS_2               3                29
  CLUS_3               0                28
  CLUS_4               2                54
D29V5, multiclass
D29V6, multiclass
        clus
vv       C15ORF2 MUTATED C15ORF2 WILD-TYPE
  CLUS_1               2                31
  CLUS_2               5               107
  CLUS_3               1                69
D29V7, multiclass
        clus
vv       C15ORF2 MUTATED C15ORF2 WILD-TYPE
  CLUS_1               1                54
  CLUS_2               1                32
  CLUS_3               3                79
  CLUS_4               3                43
D29V8, multiclass
        clus
vv       C15ORF2 MUTATED C15ORF2 WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               4                91
  CLUS_3               3               110
D29V9, multiclass
D29V10, multiclass
        clus
vv       C15ORF2 MUTATED C15ORF2 WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               2               111
  CLUS_3               5                91

Clustering(30) Variable = SPDYE5 MUTATION ANALYSIS
D30V1, multiclass
D30V2, multiclass
D30V3, multiclass
        clus
vv       SPDYE5 MUTATED SPDYE5 WILD-TYPE
  CLUS_1              1               89
  CLUS_2              3               46
  CLUS_3              0               76
D30V4, multiclass
        clus
vv       SPDYE5 MUTATED SPDYE5 WILD-TYPE
  CLUS_1              1               95
  CLUS_2              3               29
  CLUS_3              0               28
  CLUS_4              0               56
D30V5, multiclass
D30V6, multiclass
        clus
vv       SPDYE5 MUTATED SPDYE5 WILD-TYPE
  CLUS_1              0               33
  CLUS_2              4              108
  CLUS_3              0               70
D30V7, multiclass
        clus
vv       SPDYE5 MUTATED SPDYE5 WILD-TYPE
  CLUS_1              3               52
  CLUS_2              0               33
  CLUS_3              0               82
  CLUS_4              1               45
D30V8, multiclass
        clus
vv       SPDYE5 MUTATED SPDYE5 WILD-TYPE
  CLUS_1              0                8
  CLUS_2              0               95
  CLUS_3              4              109
D30V9, multiclass
D30V10, multiclass
        clus
vv       SPDYE5 MUTATED SPDYE5 WILD-TYPE
  CLUS_1              1                6
  CLUS_2              3              110
  CLUS_3              0               96

Clustering(31) Variable = SCAF1 MUTATION ANALYSIS
D31V1, multiclass
D31V2, multiclass
D31V3, multiclass
        clus
vv       SCAF1 MUTATED SCAF1 WILD-TYPE
  CLUS_1             2              88
  CLUS_2             1              48
  CLUS_3             1              75
D31V4, multiclass
        clus
vv       SCAF1 MUTATED SCAF1 WILD-TYPE
  CLUS_1             2              94
  CLUS_2             1              31
  CLUS_3             0              28
  CLUS_4             1              55
D31V5, multiclass
D31V6, multiclass
        clus
vv       SCAF1 MUTATED SCAF1 WILD-TYPE
  CLUS_1             1              32
  CLUS_2             3             109
  CLUS_3             0              70
D31V7, multiclass
        clus
vv       SCAF1 MUTATED SCAF1 WILD-TYPE
  CLUS_1             0              55
  CLUS_2             0              33
  CLUS_3             1              81
  CLUS_4             3              43
D31V8, multiclass
        clus
vv       SCAF1 MUTATED SCAF1 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             2              93
  CLUS_3             2             111
D31V9, multiclass
D31V10, multiclass
        clus
vv       SCAF1 MUTATED SCAF1 WILD-TYPE
  CLUS_1             0               7
  CLUS_2             2             111
  CLUS_3             2              94

Clustering(32) Variable = FSTL5 MUTATION ANALYSIS
D32V1, multiclass
[1] "Remove cluster labels:" "FSTL5 MUTATED"         
clus
  FSTL5 MUTATED FSTL5 WILD-TYPE 
              2              25 
     TCGA-CS-4942      TCGA-CS-4943      TCGA-CS-4944      TCGA-CS-5390 
"FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" 
     TCGA-CS-5395      TCGA-CS-5396      TCGA-DB-5270      TCGA-DB-5273 
"FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" 
     TCGA-DB-5274      TCGA-DB-5275      TCGA-DB-5276      TCGA-DB-5277 
"FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" 
     TCGA-DB-5278      TCGA-DB-5280      TCGA-DB-5281      TCGA-DH-5140 
"FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" 
     TCGA-DH-5141      TCGA-DH-5142      TCGA-DH-5143      TCGA-DH-5144 
"FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" 
     TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304      TCGA-E1-5311 
"FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" 
     TCGA-E1-5322 
"FSTL5 WILD-TYPE" 
D32V2, multiclass
[1] "Remove cluster labels:" "FSTL5 MUTATED"         
clus
  FSTL5 MUTATED FSTL5 WILD-TYPE 
              2              25 
     TCGA-CS-4942      TCGA-CS-4943      TCGA-CS-4944      TCGA-CS-5390 
"FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" 
     TCGA-CS-5395      TCGA-CS-5396      TCGA-DB-5270      TCGA-DB-5273 
"FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" 
     TCGA-DB-5274      TCGA-DB-5275      TCGA-DB-5276      TCGA-DB-5277 
"FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" 
     TCGA-DB-5278      TCGA-DB-5280      TCGA-DB-5281      TCGA-DH-5140 
"FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" 
     TCGA-DH-5141      TCGA-DH-5142      TCGA-DH-5143      TCGA-DH-5144 
"FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" 
     TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304      TCGA-E1-5311 
"FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" "FSTL5 WILD-TYPE" 
     TCGA-E1-5322 
"FSTL5 WILD-TYPE" 
D32V3, multiclass
        clus
vv       FSTL5 MUTATED FSTL5 WILD-TYPE
  CLUS_1             0              90
  CLUS_2             2              47
  CLUS_3             4              72
D32V4, multiclass
        clus
vv       FSTL5 MUTATED FSTL5 WILD-TYPE
  CLUS_1             1              95
  CLUS_2             2              30
  CLUS_3             0              28
  CLUS_4             2              54
D32V5, multiclass
D32V6, multiclass
        clus
vv       FSTL5 MUTATED FSTL5 WILD-TYPE
  CLUS_1             3              30
  CLUS_2             3             109
  CLUS_3             0              70
D32V7, multiclass
        clus
vv       FSTL5 MUTATED FSTL5 WILD-TYPE
  CLUS_1             2              53
  CLUS_2             2              31
  CLUS_3             0              82
  CLUS_4             2              44
D32V8, multiclass
        clus
vv       FSTL5 MUTATED FSTL5 WILD-TYPE
  CLUS_1             0               8
  CLUS_2             1              94
  CLUS_3             5             108
D32V9, multiclass
D32V10, multiclass
        clus
vv       FSTL5 MUTATED FSTL5 WILD-TYPE
  CLUS_1             0               7
  CLUS_2             5             108
  CLUS_3             1              95

Clustering(33) Variable = C9ORF79 MUTATION ANALYSIS
D33V1, multiclass
[1] "Remove cluster labels:" "C9ORF79 MUTATED"       
clus
  C9ORF79 MUTATED C9ORF79 WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-DB-5270        TCGA-DB-5273 
"C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" 
       TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" 
       TCGA-E1-5322 
"C9ORF79 WILD-TYPE" 
D33V2, multiclass
[1] "Remove cluster labels:" "C9ORF79 MUTATED"       
clus
  C9ORF79 MUTATED C9ORF79 WILD-TYPE 
                2                25 
       TCGA-CS-4942        TCGA-CS-4943        TCGA-CS-4944        TCGA-CS-5390 
"C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" 
       TCGA-CS-5394        TCGA-CS-5395        TCGA-DB-5270        TCGA-DB-5273 
"C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" 
       TCGA-DB-5274        TCGA-DB-5275        TCGA-DB-5276        TCGA-DB-5277 
"C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" 
       TCGA-DB-5278        TCGA-DB-5280        TCGA-DB-5281        TCGA-DH-5140 
"C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" 
       TCGA-DH-5141        TCGA-DH-5142        TCGA-DH-5143        TCGA-DH-5144 
"C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" 
       TCGA-E1-5303        TCGA-E1-5304        TCGA-E1-5311        TCGA-E1-5318 
"C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" "C9ORF79 WILD-TYPE" 
       TCGA-E1-5322 
"C9ORF79 WILD-TYPE" 
D33V3, multiclass
        clus
vv       C9ORF79 MUTATED C9ORF79 WILD-TYPE
  CLUS_1               3                87
  CLUS_2               2                47
  CLUS_3               3                73
D33V4, multiclass
        clus
vv       C9ORF79 MUTATED C9ORF79 WILD-TYPE
  CLUS_1               2                94
  CLUS_2               2                30
  CLUS_3               1                27
  CLUS_4               3                53
D33V5, multiclass
D33V6, multiclass
        clus
vv       C9ORF79 MUTATED C9ORF79 WILD-TYPE
  CLUS_1               2                31
  CLUS_2               4               108
  CLUS_3               2                68
D33V7, multiclass
        clus
vv       C9ORF79 MUTATED C9ORF79 WILD-TYPE
  CLUS_1               2                53
  CLUS_2               2                31
  CLUS_3               2                80
  CLUS_4               2                44
D33V8, multiclass
        clus
vv       C9ORF79 MUTATED C9ORF79 WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               3                92
  CLUS_3               5               108
D33V9, multiclass
D33V10, multiclass
        clus
vv       C9ORF79 MUTATED C9ORF79 WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               5               108
  CLUS_3               3                93

Clustering(34) Variable = ZCCHC12 MUTATION ANALYSIS
D34V1, multiclass
D34V2, multiclass
D34V3, multiclass
        clus
vv       ZCCHC12 MUTATED ZCCHC12 WILD-TYPE
  CLUS_1               0                90
  CLUS_2               0                49
  CLUS_3               3                73
D34V4, multiclass
        clus
vv       ZCCHC12 MUTATED ZCCHC12 WILD-TYPE
  CLUS_1               0                96
  CLUS_2               0                32
  CLUS_3               0                28
  CLUS_4               3                53
D34V5, multiclass
D34V6, multiclass
        clus
vv       ZCCHC12 MUTATED ZCCHC12 WILD-TYPE
  CLUS_1               1                32
  CLUS_2               0               112
  CLUS_3               2                68
D34V7, multiclass
        clus
vv       ZCCHC12 MUTATED ZCCHC12 WILD-TYPE
  CLUS_1               0                55
  CLUS_2               1                32
  CLUS_3               2                80
  CLUS_4               0                46
D34V8, multiclass
        clus
vv       ZCCHC12 MUTATED ZCCHC12 WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               3                92
  CLUS_3               0               113
D34V9, multiclass
D34V10, multiclass
        clus
vv       ZCCHC12 MUTATED ZCCHC12 WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               0               113
  CLUS_3               3                93

Clustering(35) Variable = SMARCA4 MUTATION ANALYSIS
D35V1, multiclass
D35V2, multiclass
D35V3, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               7                83
  CLUS_2               2                47
  CLUS_3               4                72
D35V4, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               8                88
  CLUS_2               1                31
  CLUS_3               0                28
  CLUS_4               4                52
D35V5, multiclass
D35V6, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               3                30
  CLUS_2               6               106
  CLUS_3               4                66
D35V7, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               3                52
  CLUS_2               4                29
  CLUS_3               5                77
  CLUS_4               1                45
D35V8, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               8                87
  CLUS_3               5               108
D35V9, multiclass
D35V10, multiclass
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               4               109
  CLUS_3               9                87

Clustering(36) Variable = MYH4 MUTATION ANALYSIS
D36V1, multiclass
D36V2, multiclass
D36V3, multiclass
        clus
vv       MYH4 MUTATED MYH4 WILD-TYPE
  CLUS_1            1             89
  CLUS_2            2             47
  CLUS_3            2             74
D36V4, multiclass
        clus
vv       MYH4 MUTATED MYH4 WILD-TYPE
  CLUS_1            2             94
  CLUS_2            1             31
  CLUS_3            0             28
  CLUS_4            2             54
D36V5, multiclass
D36V6, multiclass
        clus
vv       MYH4 MUTATED MYH4 WILD-TYPE
  CLUS_1            2             31
  CLUS_2            3            109
  CLUS_3            0             70
D36V7, multiclass
        clus
vv       MYH4 MUTATED MYH4 WILD-TYPE
  CLUS_1            0             55
  CLUS_2            2             31
  CLUS_3            0             82
  CLUS_4            3             43
D36V8, multiclass
        clus
vv       MYH4 MUTATED MYH4 WILD-TYPE
  CLUS_1            0              8
  CLUS_2            3             92
  CLUS_3            2            111
D36V9, multiclass
D36V10, multiclass
        clus
vv       MYH4 MUTATED MYH4 WILD-TYPE
  CLUS_1            0              7
  CLUS_2            2            111
  CLUS_3            3             93

Clustering(37) Variable = TRDN MUTATION ANALYSIS
D37V1, multiclass
D37V2, multiclass
D37V3, multiclass
        clus
vv       TRDN MUTATED TRDN WILD-TYPE
  CLUS_1            1             89
  CLUS_2            2             47
  CLUS_3            1             75
D37V4, multiclass
        clus
vv       TRDN MUTATED TRDN WILD-TYPE
  CLUS_1            2             94
  CLUS_2            1             31
  CLUS_3            0             28
  CLUS_4            1             55
D37V5, multiclass
D37V6, multiclass
        clus
vv       TRDN MUTATED TRDN WILD-TYPE
  CLUS_1            1             32
  CLUS_2            2            110
  CLUS_3            1             69
D37V7, multiclass
        clus
vv       TRDN MUTATED TRDN WILD-TYPE
  CLUS_1            1             54
  CLUS_2            0             33
  CLUS_3            2             80
  CLUS_4            1             45
D37V8, multiclass
        clus
vv       TRDN MUTATED TRDN WILD-TYPE
  CLUS_1            0              8
  CLUS_2            3             92
  CLUS_3            1            112
D37V9, multiclass
D37V10, multiclass
        clus
vv       TRDN MUTATED TRDN WILD-TYPE
  CLUS_1            0              7
  CLUS_2            1            112
  CLUS_3            3             93
                           V1                            V2 
                  "MRNA_CNMF"          "MRNA_CHIERARCHICAL" 
                           V3                            V4 
                    "CN_CNMF"            "METHLYATION_CNMF" 
                           V5                            V6 
               "MRNASEQ_CNMF"       "MRNASEQ_CHIERARCHICAL" 
                           V7                            V8 
                "MIRSEQ_CNMF"        "MIRSEQ_CHIERARCHICAL" 
                           V9                           V10 
         "MIRSEQ_MATURE_CNMF" "MIRSEQ_MATURE_CHIERARCHICAL" 
> q(save="no")
