
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/480696/GBM-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/GBM-TP/4432582/GBM-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=GBM-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=GBM-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=582, in cluster file=283, common to both=283
[1]  15 283
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
            74            209 
  EGFR MUTATED EGFR WILD-TYPE 
            74            209 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              32              251 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              32              251 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
             6            277 
  BRAF MUTATED BRAF WILD-TYPE 
             6            277 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
            14            269 
  IDH1 MUTATED IDH1 WILD-TYPE 
            14            269 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            79            204 
  TP53 MUTATED TP53 WILD-TYPE 
            79            204 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            87            196 
  PTEN MUTATED PTEN WILD-TYPE 
            87            196 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              30              253 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              30              253 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           25           258 
  RB1 MUTATED RB1 WILD-TYPE 
           25           258 
[1] "PRB2 MUTATION ANALYSIS"
[1] 3
  PRB2 MUTATED PRB2 WILD-TYPE 
             6            277 
  PRB2 MUTATED PRB2 WILD-TYPE 
             6            277 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           29           254 
  NF1 MUTATED NF1 WILD-TYPE 
           29           254 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
             12             271 
  STAG2 MUTATED STAG2 WILD-TYPE 
             12             271 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              6             277 
  CDC27 MUTATED CDC27 WILD-TYPE 
              6             277 
[1] "WNT2 MUTATION ANALYSIS"
[1] 3
  WNT2 MUTATED WNT2 WILD-TYPE 
             5            278 
  WNT2 MUTATED WNT2 WILD-TYPE 
             5            278 
[1] "TPTE2 MUTATION ANALYSIS"
[1] 3
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              8             275 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              8             275 
[1] "GABRA6 MUTATION ANALYSIS"
[1] 3
  GABRA6 MUTATED GABRA6 WILD-TYPE 
              11              272 
  GABRA6 MUTATED GABRA6 WILD-TYPE 
              11              272 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "MIR_CNMF"             
 [4] "MIR_CHIERARCHICAL"     "CN_CNMF"               "METHLYATION_CNMF"     
 [7] "RPPA_CNMF"             "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"         
[10] "MRNASEQ_CHIERARCHICAL"

Input Data has 10 rows and 283 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MIR_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MIR_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "MIR_CNMF"             
 [4] "MIR_CHIERARCHICAL"     "CN_CNMF"               "METHLYATION_CNMF"     
 [7] "RPPA_CNMF"             "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"         
[10] "MRNASEQ_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 283 columns, 0 survival variables, and 10 non-survival variables.
MRNA_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIR_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIR_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=3, 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

Clustering(1) Variable = EGFR MUTATION ANALYSIS
D1V1, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           20             49
  CLUS_2            7             36
  CLUS_3           31             43
  CLUS_4           10             44
D1V2, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           20             34
  CLUS_2           15             67
  CLUS_3           33             71
D1V3, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           20             36
  CLUS_2           23             48
  CLUS_3            6             25
  CLUS_4           11             33
D1V4, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           29             52
  CLUS_2           20             48
  CLUS_3           11             42
D1V5, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           16             71
  CLUS_2            9             69
  CLUS_3           47             61
D1V6, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            5             33
  CLUS_2           11             17
  CLUS_3            4             12
  CLUS_4            1             25
D1V7, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           13             28
  CLUS_2            5             33
  CLUS_3           16             15
  CLUS_4            2             31
D1V8, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           24             23
  CLUS_2            6             22
  CLUS_3            6             62
D1V9, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1            8             36
  CLUS_2           22             40
  CLUS_3           15             20
D1V10, multiclass
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  CLUS_1           22             39
  CLUS_2            8             13
  CLUS_3           15             44

Clustering(2) Variable = PIK3R1 MUTATION ANALYSIS
D2V1, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              7               62
  CLUS_2              2               41
  CLUS_3              8               66
  CLUS_4              5               49
D2V2, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              6               48
  CLUS_2              6               76
  CLUS_3             10               94
D2V3, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              6               50
  CLUS_2              8               63
  CLUS_3              1               30
  CLUS_4              2               42
D2V4, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              8               73
  CLUS_2              3               65
  CLUS_3              6               47
D2V5, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              5               82
  CLUS_2             12               66
  CLUS_3             14               94
D2V6, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              7               31
  CLUS_2              7               21
  CLUS_3              1               15
  CLUS_4              3               23
D2V7, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              7               34
  CLUS_2              6               32
  CLUS_3              4               27
  CLUS_4              5               28
D2V8, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              4               43
  CLUS_2              5               23
  CLUS_3             13               55
D2V9, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              5               39
  CLUS_2              6               56
  CLUS_3              1               34
D2V10, multiclass
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  CLUS_1              7               54
  CLUS_2              1               20
  CLUS_3              4               55

Clustering(3) Variable = BRAF MUTATION ANALYSIS
D3V1, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             68
  CLUS_2            1             42
  CLUS_3            2             72
  CLUS_4            0             54
D3V2, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             53
  CLUS_2            0             82
  CLUS_3            3            101
D3V3, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2             54
  CLUS_2            1             70
  CLUS_3            0             31
  CLUS_4            2             42
D3V4, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             80
  CLUS_2            4             64
  CLUS_3            0             53
D3V5, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             86
  CLUS_2            3             75
  CLUS_3            2            106
D3V6, multiclass
[1] "Remove cluster labels:" "BRAF MUTATED"          
clus
  BRAF MUTATED BRAF WILD-TYPE 
             2            106 
    TCGA-06-0650     TCGA-06-1804     TCGA-06-5408     TCGA-06-5410 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-06-5411     TCGA-06-5412     TCGA-06-5413     TCGA-06-5414 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-06-5415     TCGA-06-5417     TCGA-06-5418     TCGA-06-5856 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-06-5858     TCGA-06-5859     TCGA-06-6388     TCGA-06-6389 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-06-6390     TCGA-06-6391     TCGA-06-6693     TCGA-06-6694 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-06-6695     TCGA-06-6697     TCGA-06-6698     TCGA-06-6699 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-06-6700     TCGA-06-6701     TCGA-12-5295     TCGA-12-5299 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-12-5301     TCGA-14-0740     TCGA-14-0781     TCGA-14-0862 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-14-1043     TCGA-14-1395     TCGA-14-1450     TCGA-15-1444 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-19-5947     TCGA-19-5950     TCGA-19-5951     TCGA-19-5952 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-19-5953     TCGA-19-5954     TCGA-19-5955     TCGA-19-5958 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-19-5959     TCGA-19-5960     TCGA-26-1442     TCGA-26-5132 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-26-5133     TCGA-26-5134     TCGA-26-5135     TCGA-26-5136 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-26-5139     TCGA-26-6173     TCGA-26-6174     TCGA-28-2501 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-28-2510     TCGA-28-5204     TCGA-28-5207     TCGA-28-5208 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-28-5209     TCGA-28-5211     TCGA-28-5213     TCGA-28-5214 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-28-5215     TCGA-28-5216     TCGA-28-5218     TCGA-28-5219 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-28-5220     TCGA-28-6450     TCGA-32-1979     TCGA-32-1980 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-32-5222     TCGA-41-5651     TCGA-41-6646     TCGA-74-6573 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-74-6575     TCGA-74-6577     TCGA-74-6578     TCGA-74-6584 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-76-4925     TCGA-76-4926     TCGA-76-4927     TCGA-76-4929 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-76-4931     TCGA-76-4932     TCGA-76-4934     TCGA-76-4935 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-76-6191     TCGA-76-6192     TCGA-76-6193     TCGA-76-6280 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-76-6282     TCGA-76-6283     TCGA-76-6285     TCGA-76-6286 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-76-6656     TCGA-76-6657     TCGA-76-6660     TCGA-76-6661 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-76-6662     TCGA-76-6663     TCGA-76-6664     TCGA-81-5910 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-81-5911     TCGA-87-5896 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" 
D3V7, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             40
  CLUS_2            1             37
  CLUS_3            0             31
  CLUS_4            1             32
D3V8, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             46
  CLUS_2            2             26
  CLUS_3            0             68
D3V9, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            1             43
  CLUS_2            2             60
  CLUS_3            0             35
D3V10, multiclass
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  CLUS_1            2             59
  CLUS_2            0             21
  CLUS_3            1             58

Clustering(4) Variable = IDH1 MUTATION ANALYSIS
D4V1, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            1             68
  CLUS_2            3             40
  CLUS_3            0             74
  CLUS_4            9             45
D4V2, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             54
  CLUS_2           13             69
  CLUS_3            0            104
D4V3, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             56
  CLUS_2           10             61
  CLUS_3            0             31
  CLUS_4            0             44
D4V4, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            1             80
  CLUS_2            0             68
  CLUS_3            9             44
D4V5, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            3             84
  CLUS_2           10             68
  CLUS_3            0            108
D4V6, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             38
  CLUS_2            0             28
  CLUS_3            0             16
  CLUS_4            5             21
D4V7, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            1             40
  CLUS_2            6             32
  CLUS_3            0             31
  CLUS_4            0             33
D4V8, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             47
  CLUS_2            0             28
  CLUS_3            7             61
D4V9, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            7             37
  CLUS_2            0             62
  CLUS_3            1             34
D4V10, multiclass
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  CLUS_1            0             61
  CLUS_2            0             21
  CLUS_3            8             51

Clustering(5) Variable = TP53 MUTATION ANALYSIS
D5V1, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           16             53
  CLUS_2           19             24
  CLUS_3           11             63
  CLUS_4           22             32
D5V2, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            7             47
  CLUS_2           35             47
  CLUS_3           26             78
D5V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            8             48
  CLUS_2           32             39
  CLUS_3            7             24
  CLUS_4           15             29
D5V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           19             62
  CLUS_2           19             49
  CLUS_3           24             29
D5V5, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           35             52
  CLUS_2           27             51
  CLUS_3           16             92
D5V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            7             31
  CLUS_2            4             24
  CLUS_3            2             14
  CLUS_4           13             13
D5V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           12             29
  CLUS_2           17             21
  CLUS_3            4             27
  CLUS_4           10             23
D5V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            7             40
  CLUS_2            8             20
  CLUS_3           28             40
D5V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           23             21
  CLUS_2           13             49
  CLUS_3            8             27
D5V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1           19             42
  CLUS_2            2             19
  CLUS_3           23             36

Clustering(6) Variable = PTEN MUTATION ANALYSIS
D6V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           25             44
  CLUS_2           10             33
  CLUS_3           18             56
  CLUS_4           22             32
D6V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           13             41
  CLUS_2           28             54
  CLUS_3           34             70
D6V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           20             36
  CLUS_2           14             57
  CLUS_3           13             18
  CLUS_4           17             27
D6V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           24             57
  CLUS_2           22             46
  CLUS_3           18             35
D6V5, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           30             57
  CLUS_2           25             53
  CLUS_3           30             78
D6V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           11             27
  CLUS_2           10             18
  CLUS_3            5             11
  CLUS_4            7             19
D6V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           12             29
  CLUS_2           14             24
  CLUS_3            6             25
  CLUS_4           12             21
D6V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           11             36
  CLUS_2            9             19
  CLUS_3           24             44
D6V9, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           10             34
  CLUS_2           23             39
  CLUS_3           12             23
D6V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1           24             37
  CLUS_2            4             17
  CLUS_3           17             42

Clustering(7) Variable = PIK3CA MUTATION ANALYSIS
D7V1, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6               63
  CLUS_2              6               37
  CLUS_3             10               64
  CLUS_4              5               49
D7V2, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              7               47
  CLUS_2              7               75
  CLUS_3             13               91
D7V3, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5               51
  CLUS_2              7               64
  CLUS_3              1               30
  CLUS_4              6               38
D7V4, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6               75
  CLUS_2              8               60
  CLUS_3              5               48
D7V5, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6               81
  CLUS_2              9               69
  CLUS_3             13               95
D7V6, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              5               33
  CLUS_2              4               24
  CLUS_3              1               15
  CLUS_4              4               22
D7V7, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              3               38
  CLUS_2              5               33
  CLUS_3              2               29
  CLUS_4              4               29
D7V8, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              2               45
  CLUS_2              3               25
  CLUS_3              9               59
D7V9, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              6               38
  CLUS_2              3               59
  CLUS_3              2               33
D7V10, multiclass
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  CLUS_1              4               57
  CLUS_2              2               19
  CLUS_3              5               54

Clustering(8) Variable = RB1 MUTATION ANALYSIS
D8V1, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1          12            57
  CLUS_2           2            41
  CLUS_3           3            71
  CLUS_4           2            52
D8V2, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           1            53
  CLUS_2           3            79
  CLUS_3          15            89
D8V3, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           7            49
  CLUS_2           2            69
  CLUS_3           2            29
  CLUS_4           7            37
D8V4, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           6            75
  CLUS_2           9            59
  CLUS_3           3            50
D8V5, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           9            78
  CLUS_2          11            67
  CLUS_3           5           103
D8V6, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           6            32
  CLUS_2           2            26
  CLUS_3           0            16
  CLUS_4           0            26
D8V7, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           3            38
  CLUS_2           1            37
  CLUS_3           2            29
  CLUS_4           4            29
D8V8, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           2            45
  CLUS_2           2            26
  CLUS_3           6            62
D8V9, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           1            43
  CLUS_2           9            53
  CLUS_3           1            34
D8V10, multiclass
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  CLUS_1           9            52
  CLUS_2           0            21
  CLUS_3           2            57

Clustering(9) Variable = PRB2 MUTATION ANALYSIS
D9V1, multiclass
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            2             67
  CLUS_2            0             43
  CLUS_3            1             73
  CLUS_4            2             52
D9V2, multiclass
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            0             54
  CLUS_2            3             79
  CLUS_3            2            102
D9V3, multiclass
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            1             55
  CLUS_2            1             70
  CLUS_3            2             29
  CLUS_4            1             43
D9V4, multiclass
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            1             80
  CLUS_2            2             66
  CLUS_3            2             51
D9V5, multiclass
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  CLUS_1            1             86
  CLUS_2            2             76
  CLUS_3            3            105
D9V6, multiclass
[1] "Remove cluster labels:" "PRB2 MUTATED"          
clus
  PRB2 MUTATED PRB2 WILD-TYPE 
             1            107 
    TCGA-06-0650     TCGA-06-1804     TCGA-06-1806     TCGA-06-5408 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-5410     TCGA-06-5411     TCGA-06-5412     TCGA-06-5413 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-5414     TCGA-06-5415     TCGA-06-5417     TCGA-06-5418 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-5856     TCGA-06-5858     TCGA-06-5859     TCGA-06-6388 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-6389     TCGA-06-6390     TCGA-06-6391     TCGA-06-6693 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-6694     TCGA-06-6695     TCGA-06-6697     TCGA-06-6698 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-6699     TCGA-06-6700     TCGA-06-6701     TCGA-12-5295 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-12-5299     TCGA-12-5301     TCGA-14-0740     TCGA-14-0781 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-14-0862     TCGA-14-1043     TCGA-14-1395     TCGA-14-1450 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-15-1444     TCGA-19-5947     TCGA-19-5950     TCGA-19-5951 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-19-5952     TCGA-19-5953     TCGA-19-5954     TCGA-19-5955 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-19-5958     TCGA-19-5959     TCGA-19-5960     TCGA-26-1442 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-26-5132     TCGA-26-5133     TCGA-26-5134     TCGA-26-5135 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-26-5136     TCGA-26-5139     TCGA-26-6173     TCGA-26-6174 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-28-2501     TCGA-28-2510     TCGA-28-5204     TCGA-28-5207 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-28-5208     TCGA-28-5209     TCGA-28-5211     TCGA-28-5213 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-28-5214     TCGA-28-5215     TCGA-28-5216     TCGA-28-5218 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-28-5219     TCGA-28-5220     TCGA-28-6450     TCGA-32-1979 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-32-1980     TCGA-32-5222     TCGA-41-5651     TCGA-41-6646 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-74-6573     TCGA-74-6575     TCGA-74-6577     TCGA-74-6578 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-74-6584     TCGA-76-4925     TCGA-76-4926     TCGA-76-4927 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-4928     TCGA-76-4929     TCGA-76-4931     TCGA-76-4932 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-4934     TCGA-76-4935     TCGA-76-6191     TCGA-76-6192 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-6193     TCGA-76-6282     TCGA-76-6283     TCGA-76-6285 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-6286     TCGA-76-6656     TCGA-76-6657     TCGA-76-6660 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-6661     TCGA-76-6662     TCGA-76-6663     TCGA-76-6664 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-81-5910     TCGA-81-5911     TCGA-87-5896 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
D9V7, multiclass
[1] "Remove cluster labels:" "PRB2 MUTATED"          
clus
  PRB2 MUTATED PRB2 WILD-TYPE 
             2            141 
    TCGA-02-0003     TCGA-02-2470     TCGA-02-2485     TCGA-06-0126 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0128     TCGA-06-0129     TCGA-06-0130     TCGA-06-0154 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0155     TCGA-06-0189     TCGA-06-0238     TCGA-06-0644 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0650     TCGA-06-0875     TCGA-06-0876     TCGA-06-0877 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0878     TCGA-06-0879     TCGA-06-0882     TCGA-06-0939 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-1804     TCGA-06-1806     TCGA-06-2557     TCGA-06-2558 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-2559     TCGA-06-2562     TCGA-06-2563     TCGA-06-2564 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-2565     TCGA-06-2567     TCGA-06-2570     TCGA-06-5408 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-5410     TCGA-06-5411     TCGA-06-5412     TCGA-06-5413 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-5414     TCGA-06-5415     TCGA-06-5417     TCGA-06-5418 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-5856     TCGA-06-5858     TCGA-06-5859     TCGA-06-6388 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-6389     TCGA-06-6390     TCGA-06-6391     TCGA-06-6693 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-6694     TCGA-06-6695     TCGA-06-6697     TCGA-06-6698 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-6699     TCGA-06-6700     TCGA-06-6701     TCGA-08-0386 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-12-0692     TCGA-12-1597     TCGA-12-3649     TCGA-12-3650 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-12-3652     TCGA-12-3653     TCGA-12-5295     TCGA-12-5301 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-14-0813     TCGA-14-0862     TCGA-14-0871     TCGA-16-0846 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-19-1390     TCGA-19-1790     TCGA-19-2619     TCGA-19-2620 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-19-2625     TCGA-19-2631     TCGA-19-4068     TCGA-19-5947 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-19-5950     TCGA-19-5951     TCGA-19-5952     TCGA-19-5953 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-19-5954     TCGA-19-5955     TCGA-19-5958     TCGA-19-5959 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-19-5960     TCGA-26-1442     TCGA-26-5132     TCGA-26-5133 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-26-5134     TCGA-26-6173     TCGA-26-6174     TCGA-27-1830 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-27-1831     TCGA-27-1832     TCGA-27-1833     TCGA-27-1834 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-27-2518     TCGA-27-2528     TCGA-28-1747     TCGA-28-1753 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-28-2501     TCGA-28-5208     TCGA-28-5214     TCGA-32-1970 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-32-1982     TCGA-32-1986     TCGA-32-1991     TCGA-32-4210 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-32-4211     TCGA-32-5222     TCGA-41-2573     TCGA-41-2575 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-41-3392     TCGA-41-3393     TCGA-41-3915     TCGA-41-4097 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-41-5651     TCGA-41-6646     TCGA-74-6573     TCGA-74-6575 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-74-6577     TCGA-74-6578     TCGA-74-6584     TCGA-76-4926 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-4927     TCGA-76-4928     TCGA-76-4929     TCGA-76-4931 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-4932     TCGA-76-6192     TCGA-76-6193     TCGA-76-6282 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-6283     TCGA-76-6285     TCGA-76-6656     TCGA-76-6657 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-6660     TCGA-76-6662     TCGA-76-6663     TCGA-76-6664 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-81-5910 
"PRB2 WILD-TYPE" 
D9V8, multiclass
[1] "Remove cluster labels:" "PRB2 MUTATED"          
clus
  PRB2 MUTATED PRB2 WILD-TYPE 
             2            141 
    TCGA-02-0003     TCGA-02-2470     TCGA-02-2485     TCGA-06-0126 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0128     TCGA-06-0129     TCGA-06-0130     TCGA-06-0154 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0155     TCGA-06-0189     TCGA-06-0238     TCGA-06-0644 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0650     TCGA-06-0875     TCGA-06-0876     TCGA-06-0877 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0878     TCGA-06-0879     TCGA-06-0882     TCGA-06-0939 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-1804     TCGA-06-1806     TCGA-06-2557     TCGA-06-2558 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-2559     TCGA-06-2562     TCGA-06-2563     TCGA-06-2564 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-2565     TCGA-06-2567     TCGA-06-2570     TCGA-06-5408 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-5410     TCGA-06-5411     TCGA-06-5412     TCGA-06-5413 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-5414     TCGA-06-5415     TCGA-06-5417     TCGA-06-5418 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-5856     TCGA-06-5858     TCGA-06-5859     TCGA-06-6388 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-6389     TCGA-06-6390     TCGA-06-6391     TCGA-06-6693 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-6694     TCGA-06-6695     TCGA-06-6697     TCGA-06-6698 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-6699     TCGA-06-6700     TCGA-06-6701     TCGA-08-0386 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-12-0692     TCGA-12-1597     TCGA-12-3649     TCGA-12-3650 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-12-3652     TCGA-12-3653     TCGA-12-5295     TCGA-12-5301 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-14-0813     TCGA-14-0862     TCGA-14-0871     TCGA-16-0846 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-19-1390     TCGA-19-1790     TCGA-19-2619     TCGA-19-2620 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-19-2625     TCGA-19-2631     TCGA-19-4068     TCGA-19-5947 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-19-5950     TCGA-19-5951     TCGA-19-5952     TCGA-19-5953 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-19-5954     TCGA-19-5955     TCGA-19-5958     TCGA-19-5959 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-19-5960     TCGA-26-1442     TCGA-26-5132     TCGA-26-5133 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-26-5134     TCGA-26-6173     TCGA-26-6174     TCGA-27-1830 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-27-1831     TCGA-27-1832     TCGA-27-1833     TCGA-27-1834 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-27-2518     TCGA-27-2528     TCGA-28-1747     TCGA-28-1753 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-28-2501     TCGA-28-5208     TCGA-28-5214     TCGA-32-1970 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-32-1982     TCGA-32-1986     TCGA-32-1991     TCGA-32-4210 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-32-4211     TCGA-32-5222     TCGA-41-2573     TCGA-41-2575 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-41-3392     TCGA-41-3393     TCGA-41-3915     TCGA-41-4097 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-41-5651     TCGA-41-6646     TCGA-74-6573     TCGA-74-6575 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-74-6577     TCGA-74-6578     TCGA-74-6584     TCGA-76-4926 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-4927     TCGA-76-4928     TCGA-76-4929     TCGA-76-4931 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-4932     TCGA-76-6192     TCGA-76-6193     TCGA-76-6282 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-6283     TCGA-76-6285     TCGA-76-6656     TCGA-76-6657 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-6660     TCGA-76-6662     TCGA-76-6663     TCGA-76-6664 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-81-5910 
"PRB2 WILD-TYPE" 
D9V9, multiclass
[1] "Remove cluster labels:" "PRB2 MUTATED"          
clus
  PRB2 MUTATED PRB2 WILD-TYPE 
             2            139 
    TCGA-02-0047     TCGA-02-0055     TCGA-02-2483     TCGA-02-2485 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-02-2486     TCGA-06-0129     TCGA-06-0130     TCGA-06-0132 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0141     TCGA-06-0157     TCGA-06-0158     TCGA-06-0168 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0174     TCGA-06-0178     TCGA-06-0184     TCGA-06-0219 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0238     TCGA-06-0644     TCGA-06-0645     TCGA-06-0646 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0649     TCGA-06-0686     TCGA-06-0743     TCGA-06-0744 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0745     TCGA-06-0747     TCGA-06-0749     TCGA-06-0750 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0878     TCGA-06-0882     TCGA-06-1804     TCGA-06-2557 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-2558     TCGA-06-2559     TCGA-06-2561     TCGA-06-2562 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-2563     TCGA-06-2564     TCGA-06-2565     TCGA-06-2567 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-2569     TCGA-06-2570     TCGA-06-5408     TCGA-06-5410 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-5411     TCGA-06-5412     TCGA-06-5413     TCGA-06-5414 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-5415     TCGA-06-5417     TCGA-06-5418     TCGA-06-5856 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-5858     TCGA-06-5859     TCGA-08-0386     TCGA-12-0616 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-12-0618     TCGA-12-0619     TCGA-12-0821     TCGA-12-1597 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-12-3650     TCGA-12-3652     TCGA-12-3653     TCGA-12-5295 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-12-5299     TCGA-14-0781     TCGA-14-0787     TCGA-14-0789 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-14-0790     TCGA-14-0817     TCGA-14-1825     TCGA-14-1829 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-14-2554     TCGA-15-0742     TCGA-15-1444     TCGA-16-0846 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-16-1045     TCGA-19-1390     TCGA-19-2619     TCGA-19-2620 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-19-2624     TCGA-19-2625     TCGA-19-2629     TCGA-19-5960 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-26-1442     TCGA-26-5132     TCGA-26-5133     TCGA-26-5134 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-26-5135     TCGA-26-5136     TCGA-26-5139     TCGA-27-1830 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-27-1831     TCGA-27-1832     TCGA-27-1834     TCGA-27-1835 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-27-2519     TCGA-27-2521     TCGA-27-2523     TCGA-27-2524 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-27-2526     TCGA-27-2528     TCGA-28-1747     TCGA-28-1753 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-28-2499     TCGA-28-2509     TCGA-28-2510     TCGA-28-2513 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-28-2514     TCGA-28-5204     TCGA-28-5207     TCGA-28-5208 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-28-5209     TCGA-28-5213     TCGA-28-5215     TCGA-28-5216 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-28-5218     TCGA-28-5220     TCGA-32-1970     TCGA-32-1980 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-32-1982     TCGA-32-2615     TCGA-32-2632     TCGA-32-2634 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-32-2638     TCGA-32-4213     TCGA-32-5222     TCGA-41-2571 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-41-2572     TCGA-41-3915     TCGA-41-4097     TCGA-41-5651 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-4925     TCGA-76-4926     TCGA-76-4927     TCGA-76-4928 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-4929     TCGA-76-4931     TCGA-76-4932 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
D9V10, multiclass
[1] "Remove cluster labels:" "PRB2 MUTATED"          
clus
  PRB2 MUTATED PRB2 WILD-TYPE 
             2            139 
    TCGA-02-0047     TCGA-02-0055     TCGA-02-2483     TCGA-02-2485 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-02-2486     TCGA-06-0129     TCGA-06-0130     TCGA-06-0132 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0141     TCGA-06-0157     TCGA-06-0158     TCGA-06-0168 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0174     TCGA-06-0178     TCGA-06-0184     TCGA-06-0219 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0238     TCGA-06-0644     TCGA-06-0645     TCGA-06-0646 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0649     TCGA-06-0686     TCGA-06-0743     TCGA-06-0744 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0745     TCGA-06-0747     TCGA-06-0749     TCGA-06-0750 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-0878     TCGA-06-0882     TCGA-06-1804     TCGA-06-2557 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-2558     TCGA-06-2559     TCGA-06-2561     TCGA-06-2562 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-2563     TCGA-06-2564     TCGA-06-2565     TCGA-06-2567 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-2569     TCGA-06-2570     TCGA-06-5408     TCGA-06-5410 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-5411     TCGA-06-5412     TCGA-06-5413     TCGA-06-5414 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-5415     TCGA-06-5417     TCGA-06-5418     TCGA-06-5856 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-06-5858     TCGA-06-5859     TCGA-08-0386     TCGA-12-0616 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-12-0618     TCGA-12-0619     TCGA-12-0821     TCGA-12-1597 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-12-3650     TCGA-12-3652     TCGA-12-3653     TCGA-12-5295 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-12-5299     TCGA-14-0781     TCGA-14-0787     TCGA-14-0789 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-14-0790     TCGA-14-0817     TCGA-14-1825     TCGA-14-1829 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-14-2554     TCGA-15-0742     TCGA-15-1444     TCGA-16-0846 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-16-1045     TCGA-19-1390     TCGA-19-2619     TCGA-19-2620 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-19-2624     TCGA-19-2625     TCGA-19-2629     TCGA-19-5960 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-26-1442     TCGA-26-5132     TCGA-26-5133     TCGA-26-5134 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-26-5135     TCGA-26-5136     TCGA-26-5139     TCGA-27-1830 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-27-1831     TCGA-27-1832     TCGA-27-1834     TCGA-27-1835 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-27-2519     TCGA-27-2521     TCGA-27-2523     TCGA-27-2524 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-27-2526     TCGA-27-2528     TCGA-28-1747     TCGA-28-1753 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-28-2499     TCGA-28-2509     TCGA-28-2510     TCGA-28-2513 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-28-2514     TCGA-28-5204     TCGA-28-5207     TCGA-28-5208 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-28-5209     TCGA-28-5213     TCGA-28-5215     TCGA-28-5216 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-28-5218     TCGA-28-5220     TCGA-32-1970     TCGA-32-1980 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-32-1982     TCGA-32-2615     TCGA-32-2632     TCGA-32-2634 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-32-2638     TCGA-32-4213     TCGA-32-5222     TCGA-41-2571 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-41-2572     TCGA-41-3915     TCGA-41-4097     TCGA-41-5651 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-4925     TCGA-76-4926     TCGA-76-4927     TCGA-76-4928 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-76-4929     TCGA-76-4931     TCGA-76-4932 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 

Clustering(10) Variable = NF1 MUTATION ANALYSIS
D10V1, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1          11            58
  CLUS_2           4            39
  CLUS_3           4            70
  CLUS_4           2            52
D10V2, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            50
  CLUS_2           3            79
  CLUS_3          14            90
D10V3, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           8            48
  CLUS_2           2            69
  CLUS_3           2            29
  CLUS_4           5            39
D10V4, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           8            73
  CLUS_2           7            61
  CLUS_3           2            51
D10V5, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           4            83
  CLUS_2          17            61
  CLUS_3           8           100
D10V6, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1          11            27
  CLUS_2           1            27
  CLUS_3           0            16
  CLUS_4           1            25
D10V7, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           7            34
  CLUS_2           3            35
  CLUS_3           1            30
  CLUS_4           5            28
D10V8, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           2            45
  CLUS_2           5            23
  CLUS_3           9            59
D10V9, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           2            42
  CLUS_2           5            57
  CLUS_3           4            31
D10V10, multiclass
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  CLUS_1           5            56
  CLUS_2           2            19
  CLUS_3           4            55

Clustering(11) Variable = STAG2 MUTATION ANALYSIS
D11V1, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             4              65
  CLUS_2             3              40
  CLUS_3             1              73
  CLUS_4             2              52
D11V2, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             5              49
  CLUS_2             2              80
  CLUS_3             3             101
D11V3, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             2              54
  CLUS_2             5              66
  CLUS_3             1              30
  CLUS_4             0              44
D11V4, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             7              74
  CLUS_2             1              67
  CLUS_3             0              53
D11V5, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             5              82
  CLUS_2             3              75
  CLUS_3             4             104
D11V6, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             1              37
  CLUS_2             2              26
  CLUS_3             1              15
  CLUS_4             1              25
D11V7, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             0              41
  CLUS_2             2              36
  CLUS_3             0              31
  CLUS_4             5              28
D11V8, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             1              46
  CLUS_2             0              28
  CLUS_3             6              62
D11V9, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             1              43
  CLUS_2             3              59
  CLUS_3             3              32
D11V10, multiclass
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  CLUS_1             2              59
  CLUS_2             1              20
  CLUS_3             4              55

Clustering(12) Variable = CDC27 MUTATION ANALYSIS
D12V1, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2              67
  CLUS_2             1              42
  CLUS_3             0              74
  CLUS_4             2              52
D12V2, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             0              54
  CLUS_2             3              79
  CLUS_3             2             102
D12V3, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1              55
  CLUS_2             2              69
  CLUS_3             1              30
  CLUS_4             0              44
D12V4, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             3              78
  CLUS_2             0              68
  CLUS_3             1              52
D12V5, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             3              84
  CLUS_2             2              76
  CLUS_3             1             107
D12V6, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             0              38
  CLUS_2             1              27
  CLUS_3             0              16
  CLUS_4             2              24
D12V7, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             3              38
  CLUS_2             1              37
  CLUS_3             0              31
  CLUS_4             0              33
D12V8, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1              46
  CLUS_2             2              26
  CLUS_3             1              67
D12V9, multiclass
[1] "Remove cluster labels:" "CDC27 MUTATED"         
clus
  CDC27 MUTATED CDC27 WILD-TYPE 
              1             140 
     TCGA-02-0047      TCGA-02-0055      TCGA-02-2483      TCGA-02-2485 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-02-2486      TCGA-06-0129      TCGA-06-0130      TCGA-06-0132 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-0141      TCGA-06-0157      TCGA-06-0158      TCGA-06-0168 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-0174      TCGA-06-0178      TCGA-06-0184      TCGA-06-0219 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-0238      TCGA-06-0644      TCGA-06-0645      TCGA-06-0646 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-0649      TCGA-06-0686      TCGA-06-0743      TCGA-06-0744 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-0745      TCGA-06-0747      TCGA-06-0749      TCGA-06-0750 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-0878      TCGA-06-0882      TCGA-06-1804      TCGA-06-2557 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-2558      TCGA-06-2559      TCGA-06-2561      TCGA-06-2562 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-2563      TCGA-06-2564      TCGA-06-2565      TCGA-06-2567 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-2569      TCGA-06-2570      TCGA-06-5408      TCGA-06-5410 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-5411      TCGA-06-5412      TCGA-06-5413      TCGA-06-5414 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-5415      TCGA-06-5417      TCGA-06-5418      TCGA-06-5856 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-5858      TCGA-06-5859      TCGA-08-0386      TCGA-12-0616 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-12-0618      TCGA-12-0821      TCGA-12-1597      TCGA-12-3650 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-12-3652      TCGA-12-3653      TCGA-12-5295      TCGA-12-5299 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-14-0781      TCGA-14-0787      TCGA-14-0789      TCGA-14-0790 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-14-0817      TCGA-14-1823      TCGA-14-1825      TCGA-14-1829 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-14-2554      TCGA-15-0742      TCGA-15-1444      TCGA-16-0846 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-16-1045      TCGA-19-1390      TCGA-19-2619      TCGA-19-2620 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-19-2624      TCGA-19-2625      TCGA-19-2629      TCGA-19-5960 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-26-1442      TCGA-26-5132      TCGA-26-5133      TCGA-26-5134 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-26-5135      TCGA-26-5136      TCGA-26-5139      TCGA-27-1830 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-27-1831      TCGA-27-1832      TCGA-27-1834      TCGA-27-1835 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-27-1837      TCGA-27-2519      TCGA-27-2521      TCGA-27-2523 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-27-2524      TCGA-27-2526      TCGA-27-2528      TCGA-28-1747 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-28-1753      TCGA-28-2499      TCGA-28-2509      TCGA-28-2510 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-28-2513      TCGA-28-2514      TCGA-28-5204      TCGA-28-5207 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-28-5208      TCGA-28-5209      TCGA-28-5213      TCGA-28-5215 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-28-5216      TCGA-28-5218      TCGA-28-5220      TCGA-32-1970 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-32-1980      TCGA-32-1982      TCGA-32-2615      TCGA-32-2632 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-32-2634      TCGA-32-2638      TCGA-32-4213      TCGA-32-5222 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-41-2571      TCGA-41-2572      TCGA-41-3915      TCGA-41-4097 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-41-5651      TCGA-76-4925      TCGA-76-4926      TCGA-76-4927 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-76-4928      TCGA-76-4929      TCGA-76-4931      TCGA-76-4932 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
D12V10, multiclass
[1] "Remove cluster labels:" "CDC27 MUTATED"         
clus
  CDC27 MUTATED CDC27 WILD-TYPE 
              1             140 
     TCGA-02-0047      TCGA-02-0055      TCGA-02-2483      TCGA-02-2485 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-02-2486      TCGA-06-0129      TCGA-06-0130      TCGA-06-0132 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-0141      TCGA-06-0157      TCGA-06-0158      TCGA-06-0168 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-0174      TCGA-06-0178      TCGA-06-0184      TCGA-06-0219 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-0238      TCGA-06-0644      TCGA-06-0645      TCGA-06-0646 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-0649      TCGA-06-0686      TCGA-06-0743      TCGA-06-0744 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-0745      TCGA-06-0747      TCGA-06-0749      TCGA-06-0750 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-0878      TCGA-06-0882      TCGA-06-1804      TCGA-06-2557 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-2558      TCGA-06-2559      TCGA-06-2561      TCGA-06-2562 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-2563      TCGA-06-2564      TCGA-06-2565      TCGA-06-2567 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-2569      TCGA-06-2570      TCGA-06-5408      TCGA-06-5410 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-5411      TCGA-06-5412      TCGA-06-5413      TCGA-06-5414 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-5415      TCGA-06-5417      TCGA-06-5418      TCGA-06-5856 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-06-5858      TCGA-06-5859      TCGA-08-0386      TCGA-12-0616 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-12-0618      TCGA-12-0821      TCGA-12-1597      TCGA-12-3650 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-12-3652      TCGA-12-3653      TCGA-12-5295      TCGA-12-5299 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-14-0781      TCGA-14-0787      TCGA-14-0789      TCGA-14-0790 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-14-0817      TCGA-14-1823      TCGA-14-1825      TCGA-14-1829 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-14-2554      TCGA-15-0742      TCGA-15-1444      TCGA-16-0846 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-16-1045      TCGA-19-1390      TCGA-19-2619      TCGA-19-2620 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-19-2624      TCGA-19-2625      TCGA-19-2629      TCGA-19-5960 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-26-1442      TCGA-26-5132      TCGA-26-5133      TCGA-26-5134 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-26-5135      TCGA-26-5136      TCGA-26-5139      TCGA-27-1830 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-27-1831      TCGA-27-1832      TCGA-27-1834      TCGA-27-1835 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-27-1837      TCGA-27-2519      TCGA-27-2521      TCGA-27-2523 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-27-2524      TCGA-27-2526      TCGA-27-2528      TCGA-28-1747 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-28-1753      TCGA-28-2499      TCGA-28-2509      TCGA-28-2510 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-28-2513      TCGA-28-2514      TCGA-28-5204      TCGA-28-5207 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-28-5208      TCGA-28-5209      TCGA-28-5213      TCGA-28-5215 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-28-5216      TCGA-28-5218      TCGA-28-5220      TCGA-32-1970 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-32-1980      TCGA-32-1982      TCGA-32-2615      TCGA-32-2632 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-32-2634      TCGA-32-2638      TCGA-32-4213      TCGA-32-5222 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-41-2571      TCGA-41-2572      TCGA-41-3915      TCGA-41-4097 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-41-5651      TCGA-76-4925      TCGA-76-4926      TCGA-76-4927 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-76-4928      TCGA-76-4929      TCGA-76-4931      TCGA-76-4932 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 

Clustering(13) Variable = WNT2 MUTATION ANALYSIS
D13V1, multiclass
        clus
vv       WNT2 MUTATED WNT2 WILD-TYPE
  CLUS_1            0             69
  CLUS_2            1             42
  CLUS_3            3             71
  CLUS_4            0             54
D13V2, multiclass
        clus
vv       WNT2 MUTATED WNT2 WILD-TYPE
  CLUS_1            4             50
  CLUS_2            0             82
  CLUS_3            0            104
D13V3, multiclass
        clus
vv       WNT2 MUTATED WNT2 WILD-TYPE
  CLUS_1            1             55
  CLUS_2            1             70
  CLUS_3            0             31
  CLUS_4            1             43
D13V4, multiclass
        clus
vv       WNT2 MUTATED WNT2 WILD-TYPE
  CLUS_1            2             79
  CLUS_2            1             67
  CLUS_3            0             53
D13V5, multiclass
        clus
vv       WNT2 MUTATED WNT2 WILD-TYPE
  CLUS_1            2             85
  CLUS_2            1             77
  CLUS_3            2            106
D13V6, multiclass
[1] "Remove cluster labels:" "WNT2 MUTATED"          
clus
  WNT2 MUTATED WNT2 WILD-TYPE 
             2            106 
    TCGA-06-0650     TCGA-06-1804     TCGA-06-1806     TCGA-06-5410 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-5411     TCGA-06-5412     TCGA-06-5413     TCGA-06-5414 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-5415     TCGA-06-5417     TCGA-06-5418     TCGA-06-5856 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-5858     TCGA-06-5859     TCGA-06-6388     TCGA-06-6389 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-6390     TCGA-06-6391     TCGA-06-6693     TCGA-06-6694 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-6695     TCGA-06-6697     TCGA-06-6698     TCGA-06-6699 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-6700     TCGA-06-6701     TCGA-12-5295     TCGA-12-5299 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-12-5301     TCGA-14-0740     TCGA-14-0781     TCGA-14-0862 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-14-1043     TCGA-14-1395     TCGA-14-1450     TCGA-15-1444 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-19-5947     TCGA-19-5950     TCGA-19-5951     TCGA-19-5952 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-19-5953     TCGA-19-5954     TCGA-19-5955     TCGA-19-5958 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-19-5959     TCGA-19-5960     TCGA-26-1442     TCGA-26-5132 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-26-5133     TCGA-26-5134     TCGA-26-5135     TCGA-26-5136 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-26-5139     TCGA-26-6173     TCGA-26-6174     TCGA-28-2501 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-28-2510     TCGA-28-5204     TCGA-28-5207     TCGA-28-5208 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-28-5209     TCGA-28-5211     TCGA-28-5213     TCGA-28-5214 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-28-5215     TCGA-28-5216     TCGA-28-5218     TCGA-28-5219 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-28-5220     TCGA-28-6450     TCGA-32-1979     TCGA-32-1980 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-32-5222     TCGA-41-5651     TCGA-41-6646     TCGA-74-6573 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-74-6577     TCGA-74-6578     TCGA-74-6584     TCGA-76-4925 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-76-4926     TCGA-76-4927     TCGA-76-4928     TCGA-76-4929 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-76-4931     TCGA-76-4932     TCGA-76-4934     TCGA-76-4935 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-76-6191     TCGA-76-6192     TCGA-76-6193     TCGA-76-6280 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-76-6282     TCGA-76-6283     TCGA-76-6285     TCGA-76-6286 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-76-6656     TCGA-76-6657     TCGA-76-6660     TCGA-76-6661 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-76-6662     TCGA-76-6663     TCGA-76-6664     TCGA-81-5910 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-81-5911     TCGA-87-5896 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
D13V7, multiclass
        clus
vv       WNT2 MUTATED WNT2 WILD-TYPE
  CLUS_1            0             41
  CLUS_2            0             38
  CLUS_3            2             29
  CLUS_4            3             30
D13V8, multiclass
        clus
vv       WNT2 MUTATED WNT2 WILD-TYPE
  CLUS_1            3             44
  CLUS_2            0             28
  CLUS_3            2             66
D13V9, multiclass
[1] "Remove cluster labels:" "WNT2 MUTATED"          
clus
  WNT2 MUTATED WNT2 WILD-TYPE 
             2            139 
    TCGA-02-0047     TCGA-02-0055     TCGA-02-2483     TCGA-02-2485 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-02-2486     TCGA-06-0129     TCGA-06-0130     TCGA-06-0132 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-0141     TCGA-06-0157     TCGA-06-0158     TCGA-06-0168 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-0174     TCGA-06-0178     TCGA-06-0184     TCGA-06-0219 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-0238     TCGA-06-0644     TCGA-06-0645     TCGA-06-0646 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-0649     TCGA-06-0686     TCGA-06-0743     TCGA-06-0744 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-0745     TCGA-06-0747     TCGA-06-0749     TCGA-06-0750 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-0878     TCGA-06-0882     TCGA-06-1804     TCGA-06-2557 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-2558     TCGA-06-2559     TCGA-06-2561     TCGA-06-2562 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-2563     TCGA-06-2564     TCGA-06-2565     TCGA-06-2567 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-2569     TCGA-06-2570     TCGA-06-5410     TCGA-06-5411 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-5412     TCGA-06-5413     TCGA-06-5414     TCGA-06-5415 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-5417     TCGA-06-5418     TCGA-06-5856     TCGA-06-5858 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-5859     TCGA-08-0386     TCGA-12-0616     TCGA-12-0618 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-12-0619     TCGA-12-0821     TCGA-12-1597     TCGA-12-3650 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-12-3653     TCGA-12-5295     TCGA-12-5299     TCGA-14-0781 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-14-0787     TCGA-14-0789     TCGA-14-0790     TCGA-14-0817 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-14-1823     TCGA-14-1825     TCGA-14-1829     TCGA-14-2554 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-15-0742     TCGA-15-1444     TCGA-16-0846     TCGA-16-1045 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-19-1390     TCGA-19-2619     TCGA-19-2620     TCGA-19-2624 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-19-2625     TCGA-19-2629     TCGA-19-5960     TCGA-26-1442 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-26-5132     TCGA-26-5133     TCGA-26-5134     TCGA-26-5135 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-26-5136     TCGA-26-5139     TCGA-27-1830     TCGA-27-1831 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-27-1832     TCGA-27-1834     TCGA-27-1835     TCGA-27-1837 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-27-2519     TCGA-27-2521     TCGA-27-2523     TCGA-27-2524 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-27-2526     TCGA-27-2528     TCGA-28-1747     TCGA-28-1753 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-28-2499     TCGA-28-2509     TCGA-28-2510     TCGA-28-2513 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-28-2514     TCGA-28-5204     TCGA-28-5207     TCGA-28-5208 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-28-5209     TCGA-28-5213     TCGA-28-5215     TCGA-28-5216 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-28-5218     TCGA-28-5220     TCGA-32-1970     TCGA-32-1980 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-32-1982     TCGA-32-2615     TCGA-32-2632     TCGA-32-2634 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-32-2638     TCGA-32-4213     TCGA-32-5222     TCGA-41-2571 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-41-2572     TCGA-41-3915     TCGA-41-4097     TCGA-41-5651 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-76-4925     TCGA-76-4926     TCGA-76-4927     TCGA-76-4928 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-76-4929     TCGA-76-4931     TCGA-76-4932 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
D13V10, multiclass
[1] "Remove cluster labels:" "WNT2 MUTATED"          
clus
  WNT2 MUTATED WNT2 WILD-TYPE 
             2            139 
    TCGA-02-0047     TCGA-02-0055     TCGA-02-2483     TCGA-02-2485 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-02-2486     TCGA-06-0129     TCGA-06-0130     TCGA-06-0132 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-0141     TCGA-06-0157     TCGA-06-0158     TCGA-06-0168 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-0174     TCGA-06-0178     TCGA-06-0184     TCGA-06-0219 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-0238     TCGA-06-0644     TCGA-06-0645     TCGA-06-0646 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-0649     TCGA-06-0686     TCGA-06-0743     TCGA-06-0744 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-0745     TCGA-06-0747     TCGA-06-0749     TCGA-06-0750 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-0878     TCGA-06-0882     TCGA-06-1804     TCGA-06-2557 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-2558     TCGA-06-2559     TCGA-06-2561     TCGA-06-2562 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-2563     TCGA-06-2564     TCGA-06-2565     TCGA-06-2567 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-2569     TCGA-06-2570     TCGA-06-5410     TCGA-06-5411 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-5412     TCGA-06-5413     TCGA-06-5414     TCGA-06-5415 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-5417     TCGA-06-5418     TCGA-06-5856     TCGA-06-5858 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-06-5859     TCGA-08-0386     TCGA-12-0616     TCGA-12-0618 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-12-0619     TCGA-12-0821     TCGA-12-1597     TCGA-12-3650 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-12-3653     TCGA-12-5295     TCGA-12-5299     TCGA-14-0781 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-14-0787     TCGA-14-0789     TCGA-14-0790     TCGA-14-0817 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-14-1823     TCGA-14-1825     TCGA-14-1829     TCGA-14-2554 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-15-0742     TCGA-15-1444     TCGA-16-0846     TCGA-16-1045 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-19-1390     TCGA-19-2619     TCGA-19-2620     TCGA-19-2624 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-19-2625     TCGA-19-2629     TCGA-19-5960     TCGA-26-1442 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-26-5132     TCGA-26-5133     TCGA-26-5134     TCGA-26-5135 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-26-5136     TCGA-26-5139     TCGA-27-1830     TCGA-27-1831 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-27-1832     TCGA-27-1834     TCGA-27-1835     TCGA-27-1837 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-27-2519     TCGA-27-2521     TCGA-27-2523     TCGA-27-2524 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-27-2526     TCGA-27-2528     TCGA-28-1747     TCGA-28-1753 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-28-2499     TCGA-28-2509     TCGA-28-2510     TCGA-28-2513 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-28-2514     TCGA-28-5204     TCGA-28-5207     TCGA-28-5208 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-28-5209     TCGA-28-5213     TCGA-28-5215     TCGA-28-5216 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-28-5218     TCGA-28-5220     TCGA-32-1970     TCGA-32-1980 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-32-1982     TCGA-32-2615     TCGA-32-2632     TCGA-32-2634 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-32-2638     TCGA-32-4213     TCGA-32-5222     TCGA-41-2571 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-41-2572     TCGA-41-3915     TCGA-41-4097     TCGA-41-5651 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-76-4925     TCGA-76-4926     TCGA-76-4927     TCGA-76-4928 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 
    TCGA-76-4929     TCGA-76-4931     TCGA-76-4932 
"WNT2 WILD-TYPE" "WNT2 WILD-TYPE" "WNT2 WILD-TYPE" 

Clustering(14) Variable = TPTE2 MUTATION ANALYSIS
D14V1, multiclass
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             1              68
  CLUS_2             3              40
  CLUS_3             2              72
  CLUS_4             2              52
D14V2, multiclass
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             2              52
  CLUS_2             3              79
  CLUS_3             3             101
D14V3, multiclass
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             1              55
  CLUS_2             1              70
  CLUS_3             1              30
  CLUS_4             3              41
D14V4, multiclass
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             1              80
  CLUS_2             4              64
  CLUS_3             1              52
D14V5, multiclass
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             4              83
  CLUS_2             2              76
  CLUS_3             1             107
D14V6, multiclass
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             2              36
  CLUS_2             0              28
  CLUS_3             0              16
  CLUS_4             2              24
D14V7, multiclass
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             1              40
  CLUS_2             1              37
  CLUS_3             0              31
  CLUS_4             2              31
D14V8, multiclass
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             0              47
  CLUS_2             1              27
  CLUS_3             3              65
D14V9, multiclass
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             3              41
  CLUS_2             3              59
  CLUS_3             0              35
D14V10, multiclass
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  CLUS_1             3              58
  CLUS_2             0              21
  CLUS_3             3              56

Clustering(15) Variable = GABRA6 MUTATION ANALYSIS
D15V1, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              1               68
  CLUS_2              0               43
  CLUS_3              6               68
  CLUS_4              2               52
D15V2, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              3               51
  CLUS_2              2               80
  CLUS_3              4              100
D15V3, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              3               53
  CLUS_2              3               68
  CLUS_3              1               30
  CLUS_4              0               44
D15V4, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              4               77
  CLUS_2              1               67
  CLUS_3              2               51
D15V5, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              5               82
  CLUS_2              1               77
  CLUS_3              5              103
D15V6, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              2               36
  CLUS_2              1               27
  CLUS_3              2               14
  CLUS_4              1               25
D15V7, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              0               41
  CLUS_2              3               35
  CLUS_3              2               29
  CLUS_4              2               31
D15V8, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              3               44
  CLUS_2              0               28
  CLUS_3              4               64
D15V9, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              0               44
  CLUS_2              4               58
  CLUS_3              3               32
D15V10, multiclass
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  CLUS_1              3               58
  CLUS_2              1               20
  CLUS_3              3               56
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"              "MIR_CNMF" 
                     V4                      V5                      V6 
    "MIR_CHIERARCHICAL"               "CN_CNMF"      "METHLYATION_CNMF" 
                     V7                      V8                      V9 
            "RPPA_CNMF"    "RPPA_CHIERARCHICAL"          "MRNASEQ_CNMF" 
                    V10 
"MRNASEQ_CHIERARCHICAL" 
> q(save="no")
