
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/335038/LGG-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LGG-TP/2666685/1.GDAC_mergedClustering.Finished/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=222, in cluster file=170, common to both=170
[1]  33 170
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
           131             39 
  IDH1 MUTATED IDH1 WILD-TYPE 
           131             39 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
             6            164 
  IDH2 MUTATED IDH2 WILD-TYPE 
             6            164 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            88             82 
  TP53 MUTATED TP53 WILD-TYPE 
            88             82 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              15              155 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              15              155 
[1] "ATRX MUTATION ANALYSIS"
[1] 3
  ATRX MUTATED ATRX WILD-TYPE 
            73             97 
  ATRX MUTATED ATRX WILD-TYPE 
            73             97 
[1] "CIC MUTATION ANALYSIS"
[1] 3
  CIC MUTATED CIC WILD-TYPE 
           35           135 
  CIC MUTATED CIC WILD-TYPE 
           35           135 
[1] "FUBP1 MUTATION ANALYSIS"
[1] 3
  FUBP1 MUTATED FUBP1 WILD-TYPE 
             19             151 
  FUBP1 MUTATED FUBP1 WILD-TYPE 
             19             151 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              12              158 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              12              158 
[1] "NOTCH1 MUTATION ANALYSIS"
[1] 3
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              16              154 
  NOTCH1 MUTATED NOTCH1 WILD-TYPE 
              16              154 
[1] "ZNF844 MUTATION ANALYSIS"
[1] 3
  ZNF844 MUTATED ZNF844 WILD-TYPE 
               5              165 
  ZNF844 MUTATED ZNF844 WILD-TYPE 
               5              165 
[1] "IL32 MUTATION ANALYSIS"
[1] 3
  IL32 MUTATED IL32 WILD-TYPE 
             4            166 
  IL32 MUTATED IL32 WILD-TYPE 
             4            166 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             8            162 
  PTEN MUTATED PTEN WILD-TYPE 
             8            162 
[1] "TIMD4 MUTATION ANALYSIS"
[1] 3
  TIMD4 MUTATED TIMD4 WILD-TYPE 
              6             164 
  TIMD4 MUTATED TIMD4 WILD-TYPE 
              6             164 
[1] "CREBZF MUTATION ANALYSIS"
[1] 3
  CREBZF MUTATED CREBZF WILD-TYPE 
               4              166 
  CREBZF MUTATED CREBZF WILD-TYPE 
               4              166 
[1] "ZNF57 MUTATION ANALYSIS"
[1] 3
  ZNF57 MUTATED ZNF57 WILD-TYPE 
              6             164 
  ZNF57 MUTATED ZNF57 WILD-TYPE 
              6             164 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              159 
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              159 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           11           159 
  NF1 MUTATED NF1 WILD-TYPE 
           11           159 
[1] "TCF12 MUTATION ANALYSIS"
[1] 3
  TCF12 MUTATED TCF12 WILD-TYPE 
              6             164 
  TCF12 MUTATED TCF12 WILD-TYPE 
              6             164 
[1] "NOX4 MUTATION ANALYSIS"
[1] 3
  NOX4 MUTATED NOX4 WILD-TYPE 
             5            165 
  NOX4 MUTATED NOX4 WILD-TYPE 
             5            165 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
             8            162 
  EGFR MUTATED EGFR WILD-TYPE 
             8            162 
[1] "ZBTB20 MUTATION ANALYSIS"
[1] 3
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
               7              163 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
               7              163 
[1] "MUC7 MUTATION ANALYSIS"
[1] 3
  MUC7 MUTATED MUC7 WILD-TYPE 
             5            165 
  MUC7 MUTATED MUC7 WILD-TYPE 
             5            165 
[1] "ZNF845 MUTATION ANALYSIS"
[1] 3
  ZNF845 MUTATED ZNF845 WILD-TYPE 
               6              164 
  ZNF845 MUTATED ZNF845 WILD-TYPE 
               6              164 
[1] "ANKRD30A MUTATION ANALYSIS"
[1] 3
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 7                163 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 7                163 
[1] "SPDYE5 MUTATION ANALYSIS"
[1] 3
  SPDYE5 MUTATED SPDYE5 WILD-TYPE 
               4              166 
  SPDYE5 MUTATED SPDYE5 WILD-TYPE 
               4              166 
[1] "SCAF1 MUTATION ANALYSIS"
[1] 3
  SCAF1 MUTATED SCAF1 WILD-TYPE 
              4             166 
  SCAF1 MUTATED SCAF1 WILD-TYPE 
              4             166 
[1] "PRDM9 MUTATION ANALYSIS"
[1] 3
  PRDM9 MUTATED PRDM9 WILD-TYPE 
              5             165 
  PRDM9 MUTATED PRDM9 WILD-TYPE 
              5             165 
[1] "PRAMEF11 MUTATION ANALYSIS"
[1] 3
  PRAMEF11 MUTATED PRAMEF11 WILD-TYPE 
                 5                165 
  PRAMEF11 MUTATED PRAMEF11 WILD-TYPE 
                 5                165 
[1] "ZCCHC12 MUTATION ANALYSIS"
[1] 3
  ZCCHC12 MUTATED ZCCHC12 WILD-TYPE 
                3               167 
  ZCCHC12 MUTATED ZCCHC12 WILD-TYPE 
                3               167 
[1] "ZNF91 MUTATION ANALYSIS"
[1] 3
  ZNF91 MUTATED ZNF91 WILD-TYPE 
              5             165 
  ZNF91 MUTATED ZNF91 WILD-TYPE 
              5             165 
[1] "C3ORF35 MUTATION ANALYSIS"
[1] 3
  C3ORF35 MUTATED C3ORF35 WILD-TYPE 
                3               167 
  C3ORF35 MUTATED C3ORF35 WILD-TYPE 
                3               167 
[1] "RPTN MUTATION ANALYSIS"
[1] 3
  RPTN MUTATED RPTN WILD-TYPE 
             5            165 
  RPTN MUTATED RPTN WILD-TYPE 
             5            165 
[1] "DDX5 MUTATION ANALYSIS"
[1] 3
  DDX5 MUTATED DDX5 WILD-TYPE 
             5            165 
  DDX5 MUTATED DDX5 WILD-TYPE 
             5            165 
[1] "data2feature, selection=ALL"
[1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
[4] "METHLYATION_CNMF"      "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 8 rows and 170 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	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.
[1] "rownames(nsurv.mat)"
[1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
[4] "METHLYATION_CNMF"      "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 170 columns, 0 survival variables, and 8 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, 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

Clustering(1) Variable = IDH1 MUTATION ANALYSIS
D1V1, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            9              0
  CLUS_2            6              3
  CLUS_3            7              1
D1V2, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            9              0
  CLUS_2            6              1
  CLUS_3            7              3
D1V3, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           58              8
  CLUS_2           14             26
  CLUS_3           58              5
D1V4, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           68              2
  CLUS_2            0             30
  CLUS_3           16              2
  CLUS_4           44              4
D1V5, multiclass
D1V6, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           26              3
  CLUS_2           62             26
  CLUS_3           42              9
D1V7, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           29             11
  CLUS_2           25             13
  CLUS_3           23              4
  CLUS_4           54             11
D1V8, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1           56             10
  CLUS_2            6              4
  CLUS_3           69             25

Clustering(2) Variable = IDH2 MUTATION ANALYSIS
D2V1, multiclass
[1] "Remove cluster labels:" "IDH2 MUTATED"          
clus
  IDH2 MUTATED IDH2 WILD-TYPE 
             2             24 
    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-5395     TCGA-CS-5396     TCGA-DB-5270     TCGA-DB-5273 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DB-5274     TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DB-5278     TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144     TCGA-E1-5302 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311     TCGA-E1-5322 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
D2V2, multiclass
[1] "Remove cluster labels:" "IDH2 MUTATED"          
clus
  IDH2 MUTATED IDH2 WILD-TYPE 
             2             24 
    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-5395     TCGA-CS-5396     TCGA-DB-5270     TCGA-DB-5273 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DB-5274     TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DB-5278     TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144     TCGA-E1-5302 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
    TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311     TCGA-E1-5322 
"IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" "IDH2 WILD-TYPE" 
D2V3, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            2             64
  CLUS_2            0             40
  CLUS_3            4             59
D2V4, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            2             68
  CLUS_2            0             30
  CLUS_3            0             18
  CLUS_4            4             44
D2V5, multiclass
D2V6, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            3             26
  CLUS_2            0             88
  CLUS_3            3             48
D2V7, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            0             40
  CLUS_2            0             38
  CLUS_3            3             24
  CLUS_4            3             62
D2V8, multiclass
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  CLUS_1            3             63
  CLUS_2            0             10
  CLUS_3            3             91

Clustering(3) Variable = TP53 MUTATION ANALYSIS
D3V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8              1
  CLUS_2            4              5
  CLUS_3            5              3
D3V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8              1
  CLUS_2            4              3
  CLUS_3            5              5
D3V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           60              6
  CLUS_2           18             22
  CLUS_3           10             53
D3V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           69              1
  CLUS_2            6             24
  CLUS_3           11              7
  CLUS_4            2             46
D3V5, multiclass
D3V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             28
  CLUS_2           62             26
  CLUS_3           24             27
D3V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           26             14
  CLUS_2           28             10
  CLUS_3            5             22
  CLUS_4           29             36
D3V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           31             35
  CLUS_2            4              6
  CLUS_3           53             41

Clustering(4) Variable = PIK3CA MUTATION ANALYSIS
D4V1, multiclass
D4V2, multiclass
D4V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              0               66
  CLUS_2              4               36
  CLUS_3             11               52
D4V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              0               70
  CLUS_2              4               26
  CLUS_3              2               16
  CLUS_4              9               39
D4V5, multiclass
D4V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5               24
  CLUS_2              6               82
  CLUS_3              4               47
D4V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2               38
  CLUS_2              3               35
  CLUS_3              4               23
  CLUS_4              6               59
D4V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6               60
  CLUS_2              2                8
  CLUS_3              7               87

Clustering(5) Variable = ATRX MUTATION ANALYSIS
D5V1, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            8              1
  CLUS_2            3              6
  CLUS_3            3              5
D5V2, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            8              1
  CLUS_2            3              4
  CLUS_3            3              7
D5V3, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           48             18
  CLUS_2           15             25
  CLUS_3           10             53
D5V4, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           58             12
  CLUS_2            4             26
  CLUS_3            9              9
  CLUS_4            2             46
D5V5, multiclass
D5V6, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1            1             28
  CLUS_2           49             39
  CLUS_3           22             29
D5V7, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           18             22
  CLUS_2           27             11
  CLUS_3            3             24
  CLUS_4           25             40
D5V8, multiclass
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  CLUS_1           26             40
  CLUS_2            3              7
  CLUS_3           44             50

Clustering(6) Variable = CIC MUTATION ANALYSIS
D6V1, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0             9
  CLUS_2           4             5
  CLUS_3           2             6
D6V2, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0             9
  CLUS_2           2             5
  CLUS_3           4             6
D6V3, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           1            65
  CLUS_2           1            39
  CLUS_3          33            30
D6V4, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           0            70
  CLUS_2           1            29
  CLUS_3           2            16
  CLUS_4          31            17
D6V5, multiclass
D6V6, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1          19            10
  CLUS_2           3            85
  CLUS_3          13            38
D6V7, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1           4            36
  CLUS_2           1            37
  CLUS_3          16            11
  CLUS_4          14            51
D6V8, multiclass
        clus
vv       CIC MUTATED CIC WILD-TYPE
  CLUS_1          17            49
  CLUS_2           0            10
  CLUS_3          18            76

Clustering(7) Variable = FUBP1 MUTATION ANALYSIS
D7V1, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             3               6
  CLUS_3             0               8
D7V2, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0               9
  CLUS_2             0               7
  CLUS_3             3               7
D7V3, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0              66
  CLUS_2             1              39
  CLUS_3            18              45
D7V4, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             0              70
  CLUS_2             1              29
  CLUS_3             2              16
  CLUS_4            13              35
D7V5, multiclass
D7V6, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1            11              18
  CLUS_2             3              85
  CLUS_3             5              46
D7V7, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             2              38
  CLUS_2             1              37
  CLUS_3            10              17
  CLUS_4             6              59
D7V8, multiclass
        clus
vv       FUBP1 MUTATED FUBP1 WILD-TYPE
  CLUS_1             8              58
  CLUS_2             1               9
  CLUS_3            10              84

Clustering(8) Variable = PIK3R1 MUTATION ANALYSIS
D8V1, multiclass
[1] "Remove cluster labels:" "PIK3R1 MUTATED"        
clus
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               2               24 
      TCGA-CS-4943       TCGA-CS-5390       TCGA-CS-5395       TCGA-CS-5396 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-DB-5270       TCGA-DB-5273       TCGA-DB-5274       TCGA-DB-5275 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-DB-5276       TCGA-DB-5277       TCGA-DB-5278       TCGA-DB-5280 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-DB-5281       TCGA-DH-5140       TCGA-DH-5141       TCGA-DH-5142 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-DH-5143       TCGA-DH-5144       TCGA-E1-5302       TCGA-E1-5303 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-E1-5304       TCGA-E1-5311       TCGA-E1-5318       TCGA-E1-5322 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
D8V2, multiclass
[1] "Remove cluster labels:" "PIK3R1 MUTATED"        
clus
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               2               24 
      TCGA-CS-4943       TCGA-CS-5390       TCGA-CS-5395       TCGA-CS-5396 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-DB-5270       TCGA-DB-5273       TCGA-DB-5274       TCGA-DB-5275 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-DB-5276       TCGA-DB-5277       TCGA-DB-5278       TCGA-DB-5280 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-DB-5281       TCGA-DH-5140       TCGA-DH-5141       TCGA-DH-5142 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-DH-5143       TCGA-DH-5144       TCGA-E1-5302       TCGA-E1-5303 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-E1-5304       TCGA-E1-5311       TCGA-E1-5318       TCGA-E1-5322 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
D8V3, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              1               65
  CLUS_2              3               37
  CLUS_3              8               55
D8V4, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              2               68
  CLUS_2              2               28
  CLUS_3              1               17
  CLUS_4              5               43
D8V5, multiclass
D8V6, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              2               27
  CLUS_2              5               83
  CLUS_3              4               47
D8V7, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              4               36
  CLUS_2              2               36
  CLUS_3              2               25
  CLUS_4              4               61
D8V8, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              6               60
  CLUS_2              0               10
  CLUS_3              6               88

Clustering(9) Variable = NOTCH1 MUTATION ANALYSIS
D9V1, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              2                7
  CLUS_3              1                7
D9V2, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              0                9
  CLUS_2              1                6
  CLUS_3              2                8
D9V3, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               65
  CLUS_2              2               38
  CLUS_3             13               50
D9V4, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              2               68
  CLUS_2              1               29
  CLUS_3              0               18
  CLUS_4             12               36
D9V5, multiclass
D9V6, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              7               22
  CLUS_2              2               86
  CLUS_3              7               44
D9V7, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1              1               39
  CLUS_2              1               37
  CLUS_3              7               20
  CLUS_4              7               58
D9V8, multiclass
        clus
vv       NOTCH1 MUTATED NOTCH1 WILD-TYPE
  CLUS_1             11               55
  CLUS_2              0               10
  CLUS_3              5               89

Clustering(10) Variable = ZNF844 MUTATION ANALYSIS
D10V1, multiclass
D10V2, multiclass
D10V3, multiclass
        clus
vv       ZNF844 MUTATED ZNF844 WILD-TYPE
  CLUS_1              3               63
  CLUS_2              0               40
  CLUS_3              2               61
D10V4, multiclass
        clus
vv       ZNF844 MUTATED ZNF844 WILD-TYPE
  CLUS_1              2               68
  CLUS_2              1               29
  CLUS_3              1               17
  CLUS_4              1               47
D10V5, multiclass
D10V6, multiclass
        clus
vv       ZNF844 MUTATED ZNF844 WILD-TYPE
  CLUS_1              0               29
  CLUS_2              3               85
  CLUS_3              2               49
D10V7, multiclass
        clus
vv       ZNF844 MUTATED ZNF844 WILD-TYPE
  CLUS_1              0               40
  CLUS_2              2               36
  CLUS_3              0               27
  CLUS_4              3               62
D10V8, multiclass
        clus
vv       ZNF844 MUTATED ZNF844 WILD-TYPE
  CLUS_1              2               64
  CLUS_2              1                9
  CLUS_3              2               92

Clustering(11) Variable = IL32 MUTATION ANALYSIS
D11V1, multiclass
D11V2, multiclass
D11V3, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            0             66
  CLUS_2            2             38
  CLUS_3            2             61
D11V4, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            0             70
  CLUS_2            2             28
  CLUS_3            0             18
  CLUS_4            2             46
D11V5, multiclass
D11V6, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            1             28
  CLUS_2            2             86
  CLUS_3            1             50
D11V7, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            1             39
  CLUS_2            0             38
  CLUS_3            1             26
  CLUS_4            2             63
D11V8, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            1             65
  CLUS_2            1              9
  CLUS_3            2             92

Clustering(12) Variable = PTEN MUTATION ANALYSIS
D12V1, multiclass
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             1             25 
    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-5396     TCGA-DB-5270     TCGA-DB-5273     TCGA-DB-5274 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277     TCGA-DB-5278 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140     TCGA-DH-5141 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144     TCGA-E1-5302 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311     TCGA-E1-5318 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-E1-5322 
"PTEN WILD-TYPE" 
D12V2, multiclass
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             1             25 
    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-5396     TCGA-DB-5270     TCGA-DB-5273     TCGA-DB-5274 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277     TCGA-DB-5278 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140     TCGA-DH-5141 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144     TCGA-E1-5302 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311     TCGA-E1-5318 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-E1-5322 
"PTEN WILD-TYPE" 
D12V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             66
  CLUS_2            8             32
  CLUS_3            0             63
D12V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             70
  CLUS_2            7             23
  CLUS_3            0             18
  CLUS_4            0             48
D12V5, multiclass
D12V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             29
  CLUS_2            8             80
  CLUS_3            0             51
D12V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            5             35
  CLUS_2            3             35
  CLUS_3            0             27
  CLUS_4            0             65
D12V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            1             65
  CLUS_2            0             10
  CLUS_3            7             87

Clustering(13) Variable = TIMD4 MUTATION ANALYSIS
D13V1, multiclass
D13V2, multiclass
D13V3, multiclass
        clus
vv       TIMD4 MUTATED TIMD4 WILD-TYPE
  CLUS_1             4              62
  CLUS_2             1              39
  CLUS_3             1              62
D13V4, multiclass
        clus
vv       TIMD4 MUTATED TIMD4 WILD-TYPE
  CLUS_1             3              67
  CLUS_2             2              28
  CLUS_3             0              18
  CLUS_4             1              47
D13V5, multiclass
D13V6, multiclass
        clus
vv       TIMD4 MUTATED TIMD4 WILD-TYPE
  CLUS_1             0              29
  CLUS_2             4              84
  CLUS_3             2              49
D13V7, multiclass
        clus
vv       TIMD4 MUTATED TIMD4 WILD-TYPE
  CLUS_1             3              37
  CLUS_2             1              37
  CLUS_3             0              27
  CLUS_4             2              63
D13V8, multiclass
        clus
vv       TIMD4 MUTATED TIMD4 WILD-TYPE
  CLUS_1             2              64
  CLUS_2             0              10
  CLUS_3             4              90

Clustering(14) Variable = CREBZF MUTATION ANALYSIS
D14V1, multiclass
D14V2, multiclass
D14V3, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               66
  CLUS_2              1               39
  CLUS_3              3               60
D14V4, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               70
  CLUS_2              0               30
  CLUS_3              1               17
  CLUS_4              3               45
D14V5, multiclass
D14V6, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              1               28
  CLUS_2              0               88
  CLUS_3              3               48
D14V7, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              0               40
  CLUS_2              0               38
  CLUS_3              1               26
  CLUS_4              3               62
D14V8, multiclass
        clus
vv       CREBZF MUTATED CREBZF WILD-TYPE
  CLUS_1              4               62
  CLUS_2              0               10
  CLUS_3              0               94

Clustering(15) Variable = ZNF57 MUTATION ANALYSIS
D15V1, multiclass
D15V2, multiclass
D15V3, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             4              62
  CLUS_2             2              38
  CLUS_3             0              63
D15V4, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             4              66
  CLUS_2             2              28
  CLUS_3             0              18
  CLUS_4             0              48
D15V5, multiclass
D15V6, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             0              29
  CLUS_2             6              82
  CLUS_3             0              51
D15V7, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             3              37
  CLUS_2             3              35
  CLUS_3             0              27
  CLUS_4             0              65
D15V8, multiclass
        clus
vv       ZNF57 MUTATED ZNF57 WILD-TYPE
  CLUS_1             1              65
  CLUS_2             1               9
  CLUS_3             4              90

Clustering(16) Variable = ARID1A MUTATION ANALYSIS
D16V1, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               1               25 
      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-5395       TCGA-CS-5396       TCGA-DB-5270       TCGA-DB-5273 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DB-5274       TCGA-DB-5276       TCGA-DB-5277       TCGA-DB-5278 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DB-5280       TCGA-DB-5281       TCGA-DH-5140       TCGA-DH-5141 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144       TCGA-E1-5302 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-E1-5303       TCGA-E1-5304       TCGA-E1-5311       TCGA-E1-5318 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-E1-5322 
"ARID1A WILD-TYPE" 
D16V2, multiclass
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               1               25 
      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-5395       TCGA-CS-5396       TCGA-DB-5270       TCGA-DB-5273 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DB-5274       TCGA-DB-5276       TCGA-DB-5277       TCGA-DB-5278 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DB-5280       TCGA-DB-5281       TCGA-DH-5140       TCGA-DH-5141 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144       TCGA-E1-5302 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-E1-5303       TCGA-E1-5304       TCGA-E1-5311       TCGA-E1-5318 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-E1-5322 
"ARID1A WILD-TYPE" 
D16V3, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              5               61
  CLUS_2              1               39
  CLUS_3              4               59
D16V4, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              5               65
  CLUS_2              1               29
  CLUS_3              0               18
  CLUS_4              5               43
D16V5, multiclass
D16V6, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              3               26
  CLUS_2              3               85
  CLUS_3              4               47
D16V7, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              1               39
  CLUS_2              1               37
  CLUS_3              3               24
  CLUS_4              6               59
D16V8, multiclass
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  CLUS_1              7               59
  CLUS_2              0               10
  CLUS_3              4               90

Clustering(17) Variable = NF1 MUTATION ANALYSIS
D17V1, multiclass
[1] "Remove cluster labels:" "NF1 MUTATED"           
clus
  NF1 MUTATED NF1 WILD-TYPE 
            1            25 
   TCGA-CS-4942    TCGA-CS-4943    TCGA-CS-4944    TCGA-CS-5390    TCGA-CS-5395 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-CS-5396    TCGA-DB-5270    TCGA-DB-5273    TCGA-DB-5274    TCGA-DB-5275 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-DB-5276    TCGA-DB-5277    TCGA-DB-5278    TCGA-DB-5280    TCGA-DB-5281 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-DH-5141    TCGA-DH-5142    TCGA-DH-5143    TCGA-DH-5144    TCGA-E1-5302 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-E1-5303    TCGA-E1-5304    TCGA-E1-5311    TCGA-E1-5318    TCGA-E1-5322 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
D17V2, multiclass
[1] "Remove cluster labels:" "NF1 MUTATED"           
clus
  NF1 MUTATED NF1 WILD-TYPE 
            1            25 
   TCGA-CS-4942    TCGA-CS-4943    TCGA-CS-4944    TCGA-CS-5390    TCGA-CS-5395 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-CS-5396    TCGA-DB-5270    TCGA-DB-5273    TCGA-DB-5274    TCGA-DB-5275 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-DB-5276    TCGA-DB-5277    TCGA-DB-5278    TCGA-DB-5280    TCGA-DB-5281 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-DH-5141    TCGA-DH-5142    TCGA-DH-5143    TCGA-DH-5144    TCGA-E1-5302 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
   TCGA-E1-5303    TCGA-E1-5304    TCGA-E1-5311    TCGA-E1-5318    TCGA-E1-5322 
"NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" "NF1 WILD-TYPE" 
D17V3, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           2            64
  CLUS_2           6            34
  CLUS_3           3            60
D17V4, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           1            69
  CLUS_2           6            24
  CLUS_3           0            18
  CLUS_4           0            48
D17V5, multiclass
D17V6, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           2            27
  CLUS_2           8            80
  CLUS_3           1            50
D17V7, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           2            38
  CLUS_2           4            34
  CLUS_3           3            24
  CLUS_4           2            63
D17V8, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            62
  CLUS_2           1             9
  CLUS_3           6            88

Clustering(18) Variable = TCF12 MUTATION ANALYSIS
D18V1, multiclass
[1] "Remove cluster labels:" "TCF12 MUTATED"         
clus
  TCF12 MUTATED TCF12 WILD-TYPE 
              1              25 
     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-5395      TCGA-CS-5396      TCGA-DB-5273      TCGA-DB-5274 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-DB-5275      TCGA-DB-5276      TCGA-DB-5277      TCGA-DB-5278 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-DB-5280      TCGA-DB-5281      TCGA-DH-5140      TCGA-DH-5141 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-DH-5142      TCGA-DH-5143      TCGA-DH-5144      TCGA-E1-5302 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-E1-5303      TCGA-E1-5304      TCGA-E1-5311      TCGA-E1-5318 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-E1-5322 
"TCF12 WILD-TYPE" 
D18V2, multiclass
[1] "Remove cluster labels:" "TCF12 MUTATED"         
clus
  TCF12 MUTATED TCF12 WILD-TYPE 
              1              25 
     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-5395      TCGA-CS-5396      TCGA-DB-5273      TCGA-DB-5274 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-DB-5275      TCGA-DB-5276      TCGA-DB-5277      TCGA-DB-5278 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-DB-5280      TCGA-DB-5281      TCGA-DH-5140      TCGA-DH-5141 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-DH-5142      TCGA-DH-5143      TCGA-DH-5144      TCGA-E1-5302 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-E1-5303      TCGA-E1-5304      TCGA-E1-5311      TCGA-E1-5318 
"TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" "TCF12 WILD-TYPE" 
     TCGA-E1-5322 
"TCF12 WILD-TYPE" 
D18V3, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             3              63
  CLUS_2             1              39
  CLUS_3             2              61
D18V4, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             2              68
  CLUS_2             0              30
  CLUS_3             2              16
  CLUS_4             2              46
D18V5, multiclass
D18V6, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             2              27
  CLUS_2             2              86
  CLUS_3             2              49
D18V7, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             2              38
  CLUS_2             0              38
  CLUS_3             2              25
  CLUS_4             2              63
D18V8, multiclass
        clus
vv       TCF12 MUTATED TCF12 WILD-TYPE
  CLUS_1             2              64
  CLUS_2             1               9
  CLUS_3             3              91

Clustering(19) Variable = NOX4 MUTATION ANALYSIS
D19V1, multiclass
D19V2, multiclass
D19V3, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            0             66
  CLUS_2            2             38
  CLUS_3            3             60
D19V4, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            2             68
  CLUS_2            1             29
  CLUS_3            0             18
  CLUS_4            2             46
D19V5, multiclass
D19V6, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            1             28
  CLUS_2            1             87
  CLUS_3            3             48
D19V7, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            0             40
  CLUS_2            1             37
  CLUS_3            1             26
  CLUS_4            3             62
D19V8, multiclass
        clus
vv       NOX4 MUTATED NOX4 WILD-TYPE
  CLUS_1            4             62
  CLUS_2            0             10
  CLUS_3            1             93

Clustering(20) Variable = EGFR MUTATION ANALYSIS
D20V1, multiclass
D20V2, multiclass
D20V3, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0             66
  CLUS_2            8             32
  CLUS_3            0             63
D20V4, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0             70
  CLUS_2            8             22
  CLUS_3            0             18
  CLUS_4            0             48
D20V5, multiclass
D20V6, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            0             29
  CLUS_2            6             82
  CLUS_3            2             49
D20V7, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            1             39
  CLUS_2            5             33
  CLUS_3            0             27
  CLUS_4            2             63
D20V8, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            3             63
  CLUS_2            0             10
  CLUS_3            5             89

Clustering(21) Variable = ZBTB20 MUTATION ANALYSIS
D21V1, multiclass
D21V2, multiclass
D21V3, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              1               65
  CLUS_2              1               39
  CLUS_3              4               59
D21V4, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              1               69
  CLUS_2              1               29
  CLUS_3              0               18
  CLUS_4              4               44
D21V5, multiclass
D21V6, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              1               28
  CLUS_2              4               84
  CLUS_3              2               49
D21V7, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              1               39
  CLUS_2              2               36
  CLUS_3              1               26
  CLUS_4              3               62
D21V8, multiclass
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  CLUS_1              3               63
  CLUS_2              1                9
  CLUS_3              3               91

Clustering(22) Variable = MUC7 MUTATION ANALYSIS
D22V1, multiclass
D22V2, multiclass
D22V3, multiclass
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  CLUS_1            3             63
  CLUS_2            2             38
  CLUS_3            0             63
D22V4, multiclass
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  CLUS_1            2             68
  CLUS_2            2             28
  CLUS_3            1             17
  CLUS_4            0             48
D22V5, multiclass
D22V6, multiclass
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  CLUS_1            0             29
  CLUS_2            4             84
  CLUS_3            1             50
D22V7, multiclass
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  CLUS_1            1             39
  CLUS_2            1             37
  CLUS_3            0             27
  CLUS_4            3             62
D22V8, multiclass
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  CLUS_1            2             64
  CLUS_2            1              9
  CLUS_3            2             92

Clustering(23) Variable = ZNF845 MUTATION ANALYSIS
D23V1, multiclass
[1] "Remove cluster labels:" "ZNF845 MUTATED"        
clus
  ZNF845 MUTATED ZNF845 WILD-TYPE 
               1               25 
      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-5395       TCGA-CS-5396       TCGA-DB-5270       TCGA-DB-5273 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-DB-5274       TCGA-DB-5275       TCGA-DB-5276       TCGA-DB-5277 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-DB-5278       TCGA-DB-5280       TCGA-DH-5140       TCGA-DH-5141 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144       TCGA-E1-5302 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-E1-5303       TCGA-E1-5304       TCGA-E1-5311       TCGA-E1-5318 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-E1-5322 
"ZNF845 WILD-TYPE" 
D23V2, multiclass
[1] "Remove cluster labels:" "ZNF845 MUTATED"        
clus
  ZNF845 MUTATED ZNF845 WILD-TYPE 
               1               25 
      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-5395       TCGA-CS-5396       TCGA-DB-5270       TCGA-DB-5273 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-DB-5274       TCGA-DB-5275       TCGA-DB-5276       TCGA-DB-5277 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-DB-5278       TCGA-DB-5280       TCGA-DH-5140       TCGA-DH-5141 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-DH-5142       TCGA-DH-5143       TCGA-DH-5144       TCGA-E1-5302 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-E1-5303       TCGA-E1-5304       TCGA-E1-5311       TCGA-E1-5318 
"ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" "ZNF845 WILD-TYPE" 
      TCGA-E1-5322 
"ZNF845 WILD-TYPE" 
D23V3, multiclass
        clus
vv       ZNF845 MUTATED ZNF845 WILD-TYPE
  CLUS_1              2               64
  CLUS_2              3               37
  CLUS_3              1               62
D23V4, multiclass
        clus
vv       ZNF845 MUTATED ZNF845 WILD-TYPE
  CLUS_1              4               66
  CLUS_2              1               29
  CLUS_3              0               18
  CLUS_4              1               47
D23V5, multiclass
D23V6, multiclass
        clus
vv       ZNF845 MUTATED ZNF845 WILD-TYPE
  CLUS_1              0               29
  CLUS_2              3               85
  CLUS_3              3               48
D23V7, multiclass
        clus
vv       ZNF845 MUTATED ZNF845 WILD-TYPE
  CLUS_1              2               38
  CLUS_2              1               37
  CLUS_3              0               27
  CLUS_4              3               62
D23V8, multiclass
        clus
vv       ZNF845 MUTATED ZNF845 WILD-TYPE
  CLUS_1              4               62
  CLUS_2              1                9
  CLUS_3              1               93

Clustering(24) Variable = ANKRD30A MUTATION ANALYSIS
D24V1, multiclass
D24V2, multiclass
D24V3, multiclass
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  CLUS_1                2                 64
  CLUS_2                1                 39
  CLUS_3                4                 59
D24V4, multiclass
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  CLUS_1                2                 68
  CLUS_2                1                 29
  CLUS_3                2                 16
  CLUS_4                2                 46
D24V5, multiclass
D24V6, multiclass
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  CLUS_1                1                 28
  CLUS_2                3                 85
  CLUS_3                3                 48
D24V7, multiclass
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  CLUS_1                0                 40
  CLUS_2                2                 36
  CLUS_3                0                 27
  CLUS_4                5                 60
D24V8, multiclass
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  CLUS_1                4                 62
  CLUS_2                1                  9
  CLUS_3                2                 92

Clustering(25) Variable = SPDYE5 MUTATION ANALYSIS
D25V1, multiclass
D25V2, multiclass
D25V3, multiclass
        clus
vv       SPDYE5 MUTATED SPDYE5 WILD-TYPE
  CLUS_1              1               65
  CLUS_2              3               37
  CLUS_3              0               63
D25V4, multiclass
        clus
vv       SPDYE5 MUTATED SPDYE5 WILD-TYPE
  CLUS_1              1               69
  CLUS_2              3               27
  CLUS_3              0               18
  CLUS_4              0               48
D25V5, multiclass
D25V6, multiclass
        clus
vv       SPDYE5 MUTATED SPDYE5 WILD-TYPE
  CLUS_1              0               29
  CLUS_2              4               84
  CLUS_3              0               51
D25V7, multiclass
        clus
vv       SPDYE5 MUTATED SPDYE5 WILD-TYPE
  CLUS_1              3               37
  CLUS_2              1               37
  CLUS_3              0               27
  CLUS_4              0               65
D25V8, multiclass
        clus
vv       SPDYE5 MUTATED SPDYE5 WILD-TYPE
  CLUS_1              0               66
  CLUS_2              0               10
  CLUS_3              4               90

Clustering(26) Variable = SCAF1 MUTATION ANALYSIS
D26V1, multiclass
D26V2, multiclass
D26V3, multiclass
        clus
vv       SCAF1 MUTATED SCAF1 WILD-TYPE
  CLUS_1             2              64
  CLUS_2             1              39
  CLUS_3             1              62
D26V4, multiclass
        clus
vv       SCAF1 MUTATED SCAF1 WILD-TYPE
  CLUS_1             2              68
  CLUS_2             1              29
  CLUS_3             0              18
  CLUS_4             1              47
D26V5, multiclass
D26V6, multiclass
        clus
vv       SCAF1 MUTATED SCAF1 WILD-TYPE
  CLUS_1             1              28
  CLUS_2             3              85
  CLUS_3             0              51
D26V7, multiclass
        clus
vv       SCAF1 MUTATED SCAF1 WILD-TYPE
  CLUS_1             0              40
  CLUS_2             3              35
  CLUS_3             0              27
  CLUS_4             1              64
D26V8, multiclass
        clus
vv       SCAF1 MUTATED SCAF1 WILD-TYPE
  CLUS_1             2              64
  CLUS_2             0              10
  CLUS_3             2              92

Clustering(27) Variable = PRDM9 MUTATION ANALYSIS
D27V1, multiclass
D27V2, multiclass
D27V3, multiclass
        clus
vv       PRDM9 MUTATED PRDM9 WILD-TYPE
  CLUS_1             3              63
  CLUS_2             1              39
  CLUS_3             1              62
D27V4, multiclass
        clus
vv       PRDM9 MUTATED PRDM9 WILD-TYPE
  CLUS_1             3              67
  CLUS_2             1              29
  CLUS_3             1              17
  CLUS_4             0              48
D27V5, multiclass
D27V6, multiclass
        clus
vv       PRDM9 MUTATED PRDM9 WILD-TYPE
  CLUS_1             0              29
  CLUS_2             3              85
  CLUS_3             2              49
D27V7, multiclass
        clus
vv       PRDM9 MUTATED PRDM9 WILD-TYPE
  CLUS_1             0              40
  CLUS_2             3              35
  CLUS_3             0              27
  CLUS_4             2              63
D27V8, multiclass
        clus
vv       PRDM9 MUTATED PRDM9 WILD-TYPE
  CLUS_1             3              63
  CLUS_2             0              10
  CLUS_3             2              92

Clustering(28) Variable = PRAMEF11 MUTATION ANALYSIS
D28V1, multiclass
D28V2, multiclass
D28V3, multiclass
        clus
vv       PRAMEF11 MUTATED PRAMEF11 WILD-TYPE
  CLUS_1                3                 63
  CLUS_2                1                 39
  CLUS_3                1                 62
D28V4, multiclass
        clus
vv       PRAMEF11 MUTATED PRAMEF11 WILD-TYPE
  CLUS_1                2                 68
  CLUS_2                1                 29
  CLUS_3                1                 17
  CLUS_4                1                 47
D28V5, multiclass
D28V6, multiclass
        clus
vv       PRAMEF11 MUTATED PRAMEF11 WILD-TYPE
  CLUS_1                0                 29
  CLUS_2                2                 86
  CLUS_3                3                 48
D28V7, multiclass
        clus
vv       PRAMEF11 MUTATED PRAMEF11 WILD-TYPE
  CLUS_1                0                 40
  CLUS_2                2                 36
  CLUS_3                0                 27
  CLUS_4                3                 62
D28V8, multiclass
        clus
vv       PRAMEF11 MUTATED PRAMEF11 WILD-TYPE
  CLUS_1                5                 61
  CLUS_2                0                 10
  CLUS_3                0                 94

Clustering(29) Variable = ZCCHC12 MUTATION ANALYSIS
D29V1, multiclass
D29V2, multiclass
D29V3, multiclass
        clus
vv       ZCCHC12 MUTATED ZCCHC12 WILD-TYPE
  CLUS_1               0                66
  CLUS_2               0                40
  CLUS_3               3                60
D29V4, multiclass
        clus
vv       ZCCHC12 MUTATED ZCCHC12 WILD-TYPE
  CLUS_1               0                70
  CLUS_2               0                30
  CLUS_3               0                18
  CLUS_4               3                45
D29V5, multiclass
D29V6, multiclass
        clus
vv       ZCCHC12 MUTATED ZCCHC12 WILD-TYPE
  CLUS_1               1                28
  CLUS_2               0                88
  CLUS_3               2                49
D29V7, multiclass
        clus
vv       ZCCHC12 MUTATED ZCCHC12 WILD-TYPE
  CLUS_1               0                40
  CLUS_2               0                38
  CLUS_3               1                26
  CLUS_4               2                63
D29V8, multiclass
        clus
vv       ZCCHC12 MUTATED ZCCHC12 WILD-TYPE
  CLUS_1               3                63
  CLUS_2               0                10
  CLUS_3               0                94

Clustering(30) Variable = ZNF91 MUTATION ANALYSIS
D30V1, multiclass
D30V2, multiclass
D30V3, multiclass
        clus
vv       ZNF91 MUTATED ZNF91 WILD-TYPE
  CLUS_1             2              64
  CLUS_2             0              40
  CLUS_3             3              60
D30V4, multiclass
        clus
vv       ZNF91 MUTATED ZNF91 WILD-TYPE
  CLUS_1             0              70
  CLUS_2             2              28
  CLUS_3             0              18
  CLUS_4             3              45
D30V5, multiclass
D30V6, multiclass
        clus
vv       ZNF91 MUTATED ZNF91 WILD-TYPE
  CLUS_1             2              27
  CLUS_2             2              86
  CLUS_3             1              50
D30V7, multiclass
        clus
vv       ZNF91 MUTATED ZNF91 WILD-TYPE
  CLUS_1             1              39
  CLUS_2             1              37
  CLUS_3             1              26
  CLUS_4             2              63
D30V8, multiclass
        clus
vv       ZNF91 MUTATED ZNF91 WILD-TYPE
  CLUS_1             2              64
  CLUS_2             0              10
  CLUS_3             3              91

Clustering(31) Variable = C3ORF35 MUTATION ANALYSIS
D31V1, multiclass
D31V2, multiclass
D31V3, multiclass
        clus
vv       C3ORF35 MUTATED C3ORF35 WILD-TYPE
  CLUS_1               1                65
  CLUS_2               1                39
  CLUS_3               1                62
D31V4, multiclass
        clus
vv       C3ORF35 MUTATED C3ORF35 WILD-TYPE
  CLUS_1               1                69
  CLUS_2               1                29
  CLUS_3               0                18
  CLUS_4               1                47
D31V5, multiclass
D31V6, multiclass
        clus
vv       C3ORF35 MUTATED C3ORF35 WILD-TYPE
  CLUS_1               0                29
  CLUS_2               1                87
  CLUS_3               2                49
D31V7, multiclass
        clus
vv       C3ORF35 MUTATED C3ORF35 WILD-TYPE
  CLUS_1               0                40
  CLUS_2               1                37
  CLUS_3               0                27
  CLUS_4               2                63
D31V8, multiclass
        clus
vv       C3ORF35 MUTATED C3ORF35 WILD-TYPE
  CLUS_1               3                63
  CLUS_2               0                10
  CLUS_3               0                94

Clustering(32) Variable = RPTN MUTATION ANALYSIS
D32V1, multiclass
D32V2, multiclass
D32V3, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            1             65
  CLUS_2            3             37
  CLUS_3            1             62
D32V4, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            2             68
  CLUS_2            3             27
  CLUS_3            0             18
  CLUS_4            0             48
D32V5, multiclass
D32V6, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            0             29
  CLUS_2            3             85
  CLUS_3            1             50
D32V7, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            1             39
  CLUS_2            2             36
  CLUS_3            0             27
  CLUS_4            2             63
D32V8, multiclass
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  CLUS_1            3             63
  CLUS_2            0             10
  CLUS_3            2             92

Clustering(33) Variable = DDX5 MUTATION ANALYSIS
D33V1, multiclass
[1] "Remove cluster labels:" "DDX5 MUTATED"          
clus
  DDX5 MUTATED DDX5 WILD-TYPE 
             1             25 
    TCGA-CS-4942     TCGA-CS-4944     TCGA-CS-5390     TCGA-CS-5395 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-CS-5396     TCGA-DB-5270     TCGA-DB-5273     TCGA-DB-5274 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277     TCGA-DB-5278 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140     TCGA-DH-5141 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144     TCGA-E1-5302 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311     TCGA-E1-5318 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-E1-5322 
"DDX5 WILD-TYPE" 
D33V2, multiclass
[1] "Remove cluster labels:" "DDX5 MUTATED"          
clus
  DDX5 MUTATED DDX5 WILD-TYPE 
             1             25 
    TCGA-CS-4942     TCGA-CS-4944     TCGA-CS-5390     TCGA-CS-5395 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-CS-5396     TCGA-DB-5270     TCGA-DB-5273     TCGA-DB-5274 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-DB-5275     TCGA-DB-5276     TCGA-DB-5277     TCGA-DB-5278 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-DB-5280     TCGA-DB-5281     TCGA-DH-5140     TCGA-DH-5141 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-DH-5142     TCGA-DH-5143     TCGA-DH-5144     TCGA-E1-5302 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-E1-5303     TCGA-E1-5304     TCGA-E1-5311     TCGA-E1-5318 
"DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" "DDX5 WILD-TYPE" 
    TCGA-E1-5322 
"DDX5 WILD-TYPE" 
D33V3, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            2             64
  CLUS_2            1             39
  CLUS_3            2             61
D33V4, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            2             68
  CLUS_2            1             29
  CLUS_3            0             18
  CLUS_4            2             46
D33V5, multiclass
D33V6, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            2             27
  CLUS_2            2             86
  CLUS_3            0             51
D33V7, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            0             40
  CLUS_2            2             36
  CLUS_3            0             27
  CLUS_4            3             62
D33V8, multiclass
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  CLUS_1            4             62
  CLUS_2            0             10
  CLUS_3            1             93
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"               "CN_CNMF" 
                     V4                      V5                      V6 
     "METHLYATION_CNMF"          "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL" 
                     V7                      V8 
          "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
