
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/480640/LGG-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/LGG-TP/4431190/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=296, in cluster file=220, common to both=220
[1] "Reduce the number of clustering variables from 21 to 18."
[1]  18 220
[1] "IL32 MUTATION ANALYSIS"
[1] 3
  IL32 MUTATED IL32 WILD-TYPE 
             9            211 
  IL32 MUTATED IL32 WILD-TYPE 
             9            211 
[1] "ATRX MUTATION ANALYSIS"
[1] 3
  ATRX MUTATED ATRX WILD-TYPE 
            97            123 
  ATRX MUTATED ATRX WILD-TYPE 
            97            123 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
             8            212 
  IDH2 MUTATED IDH2 WILD-TYPE 
             8            212 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
           167             53 
  IDH1 MUTATED IDH1 WILD-TYPE 
           167             53 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           116            104 
  TP53 MUTATED TP53 WILD-TYPE 
           116            104 
[1] "CIC MUTATION ANALYSIS"
[1] 3
  CIC MUTATED CIC WILD-TYPE 
           39           181 
  CIC MUTATED CIC WILD-TYPE 
           39           181 
[1] "FUBP1 MUTATION ANALYSIS"
[1] 3
  FUBP1 MUTATED FUBP1 WILD-TYPE 
             21             199 
  FUBP1 MUTATED FUBP1 WILD-TYPE 
             21             199 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              19              201 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              19              201 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              19              201 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              19              201 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              13              207 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              13              207 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            13            207 
  PTEN MUTATED PTEN WILD-TYPE 
            13            207 
[1] "CREBZF MUTATION ANALYSIS"
[1] 3
  CREBZF MUTATED CREBZF WILD-TYPE 
               4              216 
  CREBZF MUTATED CREBZF WILD-TYPE 
               4              216 
[1] "PCDHAC2 MUTATION ANALYSIS"
[1] 3
  PCDHAC2 MUTATED PCDHAC2 WILD-TYPE 
               14               206 
  PCDHAC2 MUTATED PCDHAC2 WILD-TYPE 
               14               206 
[1] "NOX4 MUTATION ANALYSIS"
[1] 3
  NOX4 MUTATED NOX4 WILD-TYPE 
             5            215 
  NOX4 MUTATED NOX4 WILD-TYPE 
             5            215 
[1] "ZNF57 MUTATION ANALYSIS"
[1] 3
  ZNF57 MUTATED ZNF57 WILD-TYPE 
              6             214 
  ZNF57 MUTATED ZNF57 WILD-TYPE 
              6             214 
[1] "EIF1AX MUTATION ANALYSIS"
[1] 3
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               3              217 
  EIF1AX MUTATED EIF1AX WILD-TYPE 
               3              217 
[1] "DCP1B MUTATION ANALYSIS"
[1] 3
  DCP1B MUTATED DCP1B WILD-TYPE 
              4             216 
  DCP1B MUTATED DCP1B WILD-TYPE 
              4             216 
[1] "NAB2 MUTATION ANALYSIS"
[1] 3
  NAB2 MUTATED NAB2 WILD-TYPE 
             4            216 
  NAB2 MUTATED NAB2 WILD-TYPE 
             4            216 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 12 rows and 220 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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 220 columns, 0 survival variables, and 12 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=8, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = IL32 MUTATION ANALYSIS
D1V1, 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" 
D1V2, 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" 
D1V3, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            0             43
  CLUS_2            1             44
  CLUS_3            1             44
  CLUS_4            7             78
D1V4, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            2             95
  CLUS_2            2             32
  CLUS_3            5             52
  CLUS_4            0             27
D1V5, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            2             35
  CLUS_2            2             47
  CLUS_3            4             57
  CLUS_4            1             62
D1V6, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            6            101
  CLUS_3            3             94
D1V7, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            2             72
  CLUS_2            4             63
  CLUS_3            3             76
D1V8, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            2             31
  CLUS_2            4            107
  CLUS_3            3             73
D1V9, multiclass
D1V10, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            0             14
  CLUS_2            6            112
  CLUS_3            3             84
D1V11, multiclass
D1V12, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            0             35
  CLUS_2            5             82
  CLUS_3            4             93

Clustering(2) Variable = ATRX MUTATION ANALYSIS
D2V1, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            8              1
  CLUS_2            3              7
  CLUS_3            3              5
D2V2, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            1              6
  CLUS_2            3              3
  CLUS_3            8              2
  CLUS_4            2              2
D2V3, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           36              7
  CLUS_2           17             28
  CLUS_3           26             19
  CLUS_4           18             67
D2V4, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           81             16
  CLUS_2            4             30
  CLUS_3            2             55
  CLUS_4            9             18
D2V5, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           20             17
  CLUS_2           19             30
  CLUS_3           32             29
  CLUS_4           23             40
D2V6, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            3              3
  CLUS_2           49             58
  CLUS_3           42             55
D2V7, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           36             38
  CLUS_2           31             36
  CLUS_3           30             49
D2V8, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            1             32
  CLUS_2           65             46
  CLUS_3           31             45
D2V9, multiclass
D2V10, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            4             10
  CLUS_2           61             57
  CLUS_3           31             56
D2V11, multiclass
D2V12, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            9             26
  CLUS_2           49             38
  CLUS_3           38             59

Clustering(3) Variable = IDH2 MUTATION ANALYSIS
D3V1, 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" 
D3V2, 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" 
D3V3, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            0             43
  CLUS_2            0             45
  CLUS_3            2             43
  CLUS_4            6             79
D3V4, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            2             95
  CLUS_2            0             34
  CLUS_3            5             52
  CLUS_4            1             26
D3V5, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            1             36
  CLUS_2            2             47
  CLUS_3            2             59
  CLUS_4            3             60
D3V6, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            4            103
  CLUS_3            4             93
D3V7, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            0             74
  CLUS_2            3             64
  CLUS_3            5             74
D3V8, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            3             30
  CLUS_2            0            111
  CLUS_3            5             71
D3V9, multiclass
D3V10, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            0             14
  CLUS_2            3            115
  CLUS_3            5             82
D3V11, multiclass
D3V12, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            0             35
  CLUS_2            3             84
  CLUS_3            5             92

Clustering(4) Variable = IDH1 MUTATION ANALYSIS
D4V1, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            9              0
  CLUS_2            7              3
  CLUS_3            7              1
D4V2, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            5              2
  CLUS_2            6              0
  CLUS_3            9              1
  CLUS_4            3              1
D4V3, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           42              1
  CLUS_2           16             29
  CLUS_3           36              9
  CLUS_4           72             13
D4V4, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           95              2
  CLUS_2            0             34
  CLUS_3           52              5
  CLUS_4           16             11
D4V5, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           29              8
  CLUS_2           25             24
  CLUS_3           57              4
  CLUS_4           50             13
D4V6, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            6              0
  CLUS_2           76             31
  CLUS_3           79             18
D4V7, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           39             35
  CLUS_2           64              3
  CLUS_3           64             15
D4V8, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           30              3
  CLUS_2           77             34
  CLUS_3           60             16
D4V9, multiclass
D4V10, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            3             11
  CLUS_2           92             26
  CLUS_3           71             16
D4V11, multiclass
D4V12, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            6             29
  CLUS_2           76             11
  CLUS_3           84             13

Clustering(5) Variable = TP53 MUTATION ANALYSIS
D5V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8              1
  CLUS_2            4              6
  CLUS_3            5              3
D5V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1              6
  CLUS_2            4              2
  CLUS_3            8              2
  CLUS_4            4              0
D5V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           42              1
  CLUS_2           19             26
  CLUS_3           33             12
  CLUS_4           22             63
D5V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           95              2
  CLUS_2            7             27
  CLUS_3            2             55
  CLUS_4           11             16
D5V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           24             13
  CLUS_2           24             25
  CLUS_3           36             25
  CLUS_4           25             38
D5V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3              3
  CLUS_2           58             49
  CLUS_3           48             49
D5V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           44             30
  CLUS_2           37             30
  CLUS_3           35             44
D5V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             32
  CLUS_2           81             30
  CLUS_3           34             42
D5V9, multiclass
D5V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            6              8
  CLUS_2           74             44
  CLUS_3           35             52
D5V11, multiclass
D5V12, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           11             24
  CLUS_2           61             26
  CLUS_3           43             54

Clustering(6) Variable = CIC MUTATION ANALYSIS
D6V1, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0             9
  CLUS_2           5             5
  CLUS_3           2             6
D6V2, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           5             2
  CLUS_2           2             4
  CLUS_3           0            10
  CLUS_4           0             4
D6V3, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0            43
  CLUS_2           1            44
  CLUS_3           9            36
  CLUS_4          29            56
D6V4, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0            97
  CLUS_2           1            33
  CLUS_3          35            22
  CLUS_4           2            25
D6V5, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           1            36
  CLUS_2           4            45
  CLUS_3          20            41
  CLUS_4          14            49
D6V6, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           2             4
  CLUS_2          20            87
  CLUS_3          17            80
D6V7, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           2            72
  CLUS_2          18            49
  CLUS_3          19            60
D6V8, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1          22            11
  CLUS_2           1           110
  CLUS_3          16            60
D6V9, multiclass
D6V10, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           1            13
  CLUS_2          19            99
  CLUS_3          19            68
D6V11, multiclass
D6V12, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           2            33
  CLUS_2          14            73
  CLUS_3          23            74

Clustering(7) Variable = FUBP1 MUTATION ANALYSIS
D7V1, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             4               6
  CLUS_3             0               8
D7V2, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             4               3
  CLUS_2             0               6
  CLUS_3             0              10
  CLUS_4             0               4
D7V3, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0              43
  CLUS_2             1              44
  CLUS_3             3              42
  CLUS_4            17              68
D7V4, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0              97
  CLUS_2             1              33
  CLUS_3            17              40
  CLUS_4             0              27
D7V5, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             1              36
  CLUS_2             2              47
  CLUS_3             9              52
  CLUS_4             9              54
D7V6, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             1               5
  CLUS_2            10              97
  CLUS_3            10              87
D7V7, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             2              72
  CLUS_2            11              56
  CLUS_3             8              71
D7V8, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1            12              21
  CLUS_2             2             109
  CLUS_3             7              69
D7V9, multiclass
D7V10, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             1              13
  CLUS_2            11             107
  CLUS_3             9              78
D7V11, multiclass
D7V12, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             2              33
  CLUS_2             7              80
  CLUS_3            12              85

Clustering(8) Variable = NOTCH1 MUTATION ANALYSIS
D8V1, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              2                8
  CLUS_3              1                7
D8V2, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              2                5
  CLUS_2              1                5
  CLUS_3              0               10
  CLUS_4              0                4
D8V3, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               42
  CLUS_2              1               44
  CLUS_3              5               40
  CLUS_4             12               73
D8V4, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              3               94
  CLUS_2              1               33
  CLUS_3             14               43
  CLUS_4              0               27
D8V5, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              0               37
  CLUS_2              4               45
  CLUS_3              7               54
  CLUS_4              8               55
D8V6, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              9               98
  CLUS_3             10               87
D8V7, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              2               72
  CLUS_2              7               60
  CLUS_3             10               69
D8V8, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              8               25
  CLUS_2              3              108
  CLUS_3              8               68
D8V9, multiclass
D8V10, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               13
  CLUS_2              6              112
  CLUS_3             12               75
D8V11, multiclass
D8V12, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               34
  CLUS_2              5               82
  CLUS_3             13               84

Clustering(9) Variable = PIK3CA MUTATION ANALYSIS
D9V1, multiclass
D9V2, multiclass
D9V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1               42
  CLUS_2              4               41
  CLUS_3              6               39
  CLUS_4              8               77
D9V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1               96
  CLUS_2              5               29
  CLUS_3             11               46
  CLUS_4              2               25
D9V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3               34
  CLUS_2              6               43
  CLUS_3              4               57
  CLUS_4              6               57
D9V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2                4
  CLUS_2              7              100
  CLUS_3             10               87
D9V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6               68
  CLUS_2              6               61
  CLUS_3              7               72
D9V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5               28
  CLUS_2              8              103
  CLUS_3              6               70
D9V9, multiclass
D9V10, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              1               13
  CLUS_2              9              109
  CLUS_3              9               78
D9V11, multiclass
D9V12, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5               30
  CLUS_2              5               82
  CLUS_3              9               88

Clustering(10) Variable = PIK3R1 MUTATION ANALYSIS
D10V1, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              2                7
  CLUS_2              1                9
  CLUS_3              0                8
D10V2, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              1                6
  CLUS_2              0                6
  CLUS_3              2                8
  CLUS_4              0                4
D10V3, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              0               43
  CLUS_2              3               42
  CLUS_3              2               43
  CLUS_4              8               77
D10V4, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              3               94
  CLUS_2              2               32
  CLUS_3              7               50
  CLUS_4              0               27
D10V5, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              3               34
  CLUS_2              1               48
  CLUS_3              5               56
  CLUS_4              4               59
D10V6, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              0                6
  CLUS_2              7              100
  CLUS_3              6               91
D10V7, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              3               71
  CLUS_2              5               62
  CLUS_3              5               74
D10V8, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              3               30
  CLUS_2              4              107
  CLUS_3              6               70
D10V9, multiclass
D10V10, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              1               13
  CLUS_2              7              111
  CLUS_3              5               82
D10V11, multiclass
D10V12, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              2               33
  CLUS_2              6               81
  CLUS_3              5               92

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             43
  CLUS_2           11             34
  CLUS_3            2             43
  CLUS_4            0             85
D11V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             97
  CLUS_2           12             22
  CLUS_3            0             57
  CLUS_4            0             27
D11V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             36
  CLUS_2            8             41
  CLUS_3            2             59
  CLUS_4            0             63
D11V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0              6
  CLUS_2           11             96
  CLUS_3            0             97
D11V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           13             61
  CLUS_2            0             67
  CLUS_3            0             79
D11V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             33
  CLUS_2           13             98
  CLUS_3            0             76
D11V9, multiclass
D11V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             10
  CLUS_2            9            109
  CLUS_3            0             87
D11V11, multiclass
D11V12, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            9             26
  CLUS_2            4             83
  CLUS_3            0             97

Clustering(12) Variable = CREBZF MUTATION ANALYSIS
D12V1, multiclass
D12V2, multiclass
D12V3, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               43
  CLUS_2              0               45
  CLUS_3              2               43
  CLUS_4              2               83
D12V4, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               97
  CLUS_2              0               34
  CLUS_3              3               54
  CLUS_4              1               26
D12V5, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               37
  CLUS_2              1               48
  CLUS_3              0               61
  CLUS_4              3               60
D12V6, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0                6
  CLUS_2              0              107
  CLUS_3              4               93
D12V7, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               74
  CLUS_2              0               67
  CLUS_3              4               75
D12V8, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              1               32
  CLUS_2              0              111
  CLUS_3              3               73
D12V9, multiclass
D12V10, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               14
  CLUS_2              0              118
  CLUS_3              4               83
D12V11, multiclass
D12V12, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               35
  CLUS_2              0               87
  CLUS_3              4               93

Clustering(13) Variable = PCDHAC2 MUTATION ANALYSIS
D13V1, multiclass
        clus
vv       PCDHAC2 MUTATED PCDHAC2 WILD-TYPE
  CLUS_1               1                 8
  CLUS_2               1                 9
  CLUS_3               1                 7
D13V2, multiclass
        clus
vv       PCDHAC2 MUTATED PCDHAC2 WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               1                 5
  CLUS_3               1                 9
  CLUS_4               0                 4
D13V3, multiclass
        clus
vv       PCDHAC2 MUTATED PCDHAC2 WILD-TYPE
  CLUS_1               0                43
  CLUS_2               6                39
  CLUS_3               5                40
  CLUS_4               3                82
D13V4, multiclass
        clus
vv       PCDHAC2 MUTATED PCDHAC2 WILD-TYPE
  CLUS_1               5                92
  CLUS_2               6                28
  CLUS_3               1                56
  CLUS_4               2                25
D13V5, multiclass
        clus
vv       PCDHAC2 MUTATED PCDHAC2 WILD-TYPE
  CLUS_1               3                34
  CLUS_2               4                45
  CLUS_3               2                59
  CLUS_4               4                59
D13V6, multiclass
        clus
vv       PCDHAC2 MUTATED PCDHAC2 WILD-TYPE
  CLUS_1               1                 5
  CLUS_2               5               102
  CLUS_3               7                90
D13V7, multiclass
        clus
vv       PCDHAC2 MUTATED PCDHAC2 WILD-TYPE
  CLUS_1               5                69
  CLUS_2               5                62
  CLUS_3               4                75
D13V8, multiclass
        clus
vv       PCDHAC2 MUTATED PCDHAC2 WILD-TYPE
  CLUS_1               1                32
  CLUS_2               8               103
  CLUS_3               5                71
D13V9, multiclass
D13V10, multiclass
        clus
vv       PCDHAC2 MUTATED PCDHAC2 WILD-TYPE
  CLUS_1               3                11
  CLUS_2               7               111
  CLUS_3               4                83
D13V11, multiclass
D13V12, multiclass
        clus
vv       PCDHAC2 MUTATED PCDHAC2 WILD-TYPE
  CLUS_1               5                30
  CLUS_2               6                81
  CLUS_3               3                94

Clustering(14) Variable = NOX4 MUTATION ANALYSIS
D14V1, multiclass
D14V2, multiclass
D14V3, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            0             43
  CLUS_2            1             44
  CLUS_3            3             42
  CLUS_4            1             84
D14V4, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            2             95
  CLUS_2            1             33
  CLUS_3            2             55
  CLUS_4            0             27
D14V5, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            0             37
  CLUS_2            0             49
  CLUS_3            3             58
  CLUS_4            2             61
D14V6, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            0              6
  CLUS_2            2            105
  CLUS_3            3             94
D14V7, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            2             72
  CLUS_2            0             67
  CLUS_3            3             76
D14V8, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            1             32
  CLUS_2            1            110
  CLUS_3            3             73
D14V9, multiclass
D14V10, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            1             13
  CLUS_2            1            117
  CLUS_3            3             84
D14V11, multiclass
D14V12, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            1             34
  CLUS_2            1             86
  CLUS_3            3             94

Clustering(15) Variable = ZNF57 MUTATION ANALYSIS
D15V1, multiclass
D15V2, multiclass
D15V3, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             3              40
  CLUS_2             2              43
  CLUS_3             0              45
  CLUS_4             1              84
D15V4, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             4              93
  CLUS_2             2              32
  CLUS_3             0              57
  CLUS_4             0              27
D15V5, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             1              36
  CLUS_2             2              47
  CLUS_3             2              59
  CLUS_4             0              63
D15V6, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             0               6
  CLUS_2             5             102
  CLUS_3             0              97
D15V7, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             5              69
  CLUS_2             1              66
  CLUS_3             0              79
D15V8, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             0              33
  CLUS_2             6             105
  CLUS_3             0              76
D15V9, multiclass
D15V10, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             1              13
  CLUS_2             5             113
  CLUS_3             0              87
D15V11, multiclass
D15V12, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             1              34
  CLUS_2             5              82
  CLUS_3             0              97

Clustering(16) Variable = EIF1AX MUTATION ANALYSIS
D16V1, multiclass
D16V2, multiclass
D16V3, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               43
  CLUS_2              1               44
  CLUS_3              1               44
  CLUS_4              1               84
D16V4, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              3               94
  CLUS_2              0               34
  CLUS_3              0               57
  CLUS_4              0               27
D16V5, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               37
  CLUS_2              0               49
  CLUS_3              2               59
  CLUS_4              1               62
D16V6, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0                6
  CLUS_2              2              105
  CLUS_3              1               96
D16V7, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              1               73
  CLUS_2              1               66
  CLUS_3              1               78
D16V8, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               33
  CLUS_2              2              109
  CLUS_3              1               75
D16V9, multiclass
D16V10, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               14
  CLUS_2              3              115
  CLUS_3              0               87
D16V11, multiclass
D16V12, multiclass
        clus
vv       EIF1AX MUTATED EIF1AX WILD-TYPE
  CLUS_1              0               35
  CLUS_2              2               85
  CLUS_3              1               96

Clustering(17) Variable = DCP1B MUTATION ANALYSIS
D17V1, multiclass
[1] "Remove cluster labels:" "DCP1B MUTATED"         
clus
  DCP1B MUTATED DCP1B WILD-TYPE 
              1              26 
     TCGA-CS-4942      TCGA-CS-4943      TCGA-CS-4944      TCGA-CS-5390 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-CS-5394      TCGA-CS-5395      TCGA-CS-5396      TCGA-DB-5270 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-DB-5273      TCGA-DB-5274      TCGA-DB-5275      TCGA-DB-5276 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-DB-5277      TCGA-DB-5278      TCGA-DB-5280      TCGA-DB-5281 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-DH-5140      TCGA-DH-5141      TCGA-DH-5142      TCGA-DH-5144 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304      TCGA-E1-5311 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-E1-5318      TCGA-E1-5322 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
D17V2, multiclass
[1] "Remove cluster labels:" "DCP1B MUTATED"         
clus
  DCP1B MUTATED DCP1B WILD-TYPE 
              1              26 
     TCGA-CS-4942      TCGA-CS-4943      TCGA-CS-4944      TCGA-CS-5390 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-CS-5394      TCGA-CS-5395      TCGA-CS-5396      TCGA-DB-5270 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-DB-5273      TCGA-DB-5274      TCGA-DB-5275      TCGA-DB-5276 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-DB-5277      TCGA-DB-5278      TCGA-DB-5280      TCGA-DB-5281 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-DH-5140      TCGA-DH-5141      TCGA-DH-5142      TCGA-DH-5144 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-E1-5302      TCGA-E1-5303      TCGA-E1-5304      TCGA-E1-5311 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-E1-5318      TCGA-E1-5322 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
D17V3, multiclass
        clus
vv       DCP1B MUTATED DCP1B WILD-TYPE
  CLUS_1             0              43
  CLUS_2             0              45
  CLUS_3             0              45
  CLUS_4             4              81
D17V4, multiclass
        clus
vv       DCP1B MUTATED DCP1B WILD-TYPE
  CLUS_1             1              96
  CLUS_2             0              34
  CLUS_3             2              55
  CLUS_4             1              26
D17V5, multiclass
        clus
vv       DCP1B MUTATED DCP1B WILD-TYPE
  CLUS_1             3              34
  CLUS_2             0              49
  CLUS_3             1              60
  CLUS_4             0              63
D17V6, multiclass
        clus
vv       DCP1B MUTATED DCP1B WILD-TYPE
  CLUS_1             0               6
  CLUS_2             0             107
  CLUS_3             4              93
D17V7, multiclass
        clus
vv       DCP1B MUTATED DCP1B WILD-TYPE
  CLUS_1             1              73
  CLUS_2             1              66
  CLUS_3             2              77
D17V8, multiclass
        clus
vv       DCP1B MUTATED DCP1B WILD-TYPE
  CLUS_1             0              33
  CLUS_2             2             109
  CLUS_3             2              74
D17V9, multiclass
D17V10, multiclass
        clus
vv       DCP1B MUTATED DCP1B WILD-TYPE
  CLUS_1             0              14
  CLUS_2             1             117
  CLUS_3             3              84
D17V11, multiclass
D17V12, multiclass
        clus
vv       DCP1B MUTATED DCP1B WILD-TYPE
  CLUS_1             0              35
  CLUS_2             1              86
  CLUS_3             3              94

Clustering(18) Variable = NAB2 MUTATION ANALYSIS
D18V1, multiclass
D18V2, multiclass
D18V3, multiclass
        clus
vv       NAB2 MUTATED NAB2 WILD-TYPE
  CLUS_1            0             43
  CLUS_2            1             44
  CLUS_3            1             44
  CLUS_4            2             83
D18V4, multiclass
        clus
vv       NAB2 MUTATED NAB2 WILD-TYPE
  CLUS_1            1             96
  CLUS_2            0             34
  CLUS_3            3             54
  CLUS_4            0             27
D18V5, multiclass
        clus
vv       NAB2 MUTATED NAB2 WILD-TYPE
  CLUS_1            0             37
  CLUS_2            0             49
  CLUS_3            2             59
  CLUS_4            2             61
D18V6, multiclass
        clus
vv       NAB2 MUTATED NAB2 WILD-TYPE
  CLUS_1            1              5
  CLUS_2            2            105
  CLUS_3            1             96
D18V7, multiclass
        clus
vv       NAB2 MUTATED NAB2 WILD-TYPE
  CLUS_1            1             73
  CLUS_2            2             65
  CLUS_3            1             78
D18V8, multiclass
        clus
vv       NAB2 MUTATED NAB2 WILD-TYPE
  CLUS_1            2             31
  CLUS_2            1            110
  CLUS_3            1             75
D18V9, multiclass
D18V10, multiclass
        clus
vv       NAB2 MUTATED NAB2 WILD-TYPE
  CLUS_1            0             14
  CLUS_2            3            115
  CLUS_3            1             86
D18V11, multiclass
D18V12, multiclass
        clus
vv       NAB2 MUTATED NAB2 WILD-TYPE
  CLUS_1            0             35
  CLUS_2            2             85
  CLUS_3            2             95
                           V1                            V2 
                  "MRNA_CNMF"          "MRNA_CHIERARCHICAL" 
                           V3                            V4 
                    "CN_CNMF"            "METHLYATION_CNMF" 
                           V5                            V6 
                  "RPPA_CNMF"          "RPPA_CHIERARCHICAL" 
                           V7                            V8 
               "MRNASEQ_CNMF"       "MRNASEQ_CHIERARCHICAL" 
                           V9                           V10 
                "MIRSEQ_CNMF"        "MIRSEQ_CHIERARCHICAL" 
                          V11                           V12 
         "MIRSEQ_MATURE_CNMF" "MIRSEQ_MATURE_CHIERARCHICAL" 
> q(save="no")
