
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/423668/KIRC-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/KIRC-TP/3536964/KIRC-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KIRC-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=KIRC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=513, in cluster file=293, common to both=293
[1]  10 293
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            107             186 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            107             186 
[1] "SV2C MUTATION ANALYSIS"
[1] 3
  SV2C MUTATED SV2C WILD-TYPE 
             3            290 
  SV2C MUTATED SV2C WILD-TYPE 
             3            290 
[1] "VHL MUTATION ANALYSIS"
[1] 3
  VHL MUTATED VHL WILD-TYPE 
          138           155 
  VHL MUTATED VHL WILD-TYPE 
          138           155 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
            27            266 
  BAP1 MUTATED BAP1 WILD-TYPE 
            27            266 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             34             259 
  SETD2 MUTATED SETD2 WILD-TYPE 
             34             259 
[1] "KDM5C MUTATION ANALYSIS"
[1] 3
  KDM5C MUTATED KDM5C WILD-TYPE 
             18             275 
  KDM5C MUTATED KDM5C WILD-TYPE 
             18             275 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             6            287 
  TP53 MUTATED TP53 WILD-TYPE 
             6            287 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             9            284 
  PTEN MUTATED PTEN WILD-TYPE 
             9            284 
[1] "EBPL MUTATION ANALYSIS"
[1] 3
  EBPL MUTATED EBPL WILD-TYPE 
             6            287 
  EBPL MUTATED EBPL WILD-TYPE 
             6            287 
[1] "TOR1A MUTATION ANALYSIS"
[1] 3
  TOR1A MUTATED TOR1A WILD-TYPE 
              3             290 
  TOR1A MUTATED TOR1A WILD-TYPE 
              3             290 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 12 rows and 293 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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 293 columns, 0 survival variables, and 12 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=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=6, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = PBRM1 MUTATION ANALYSIS
D1V1, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1            14              11
  CLUS_2             4              17
  CLUS_3             1               2
D1V2, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             1               3
  CLUS_2            14              11
  CLUS_3             4              16
D1V3, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1            43              50
  CLUS_2            53              81
  CLUS_3            11              54
D1V4, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1            36              35
  CLUS_2            30              53
  CLUS_3             8              37
D1V5, multiclass
D1V6, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1            41              76
  CLUS_2            39              66
  CLUS_3            21              31
D1V7, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1            58              66
  CLUS_2            34              76
  CLUS_3             8              38
D1V8, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             8              23
  CLUS_2            56              76
  CLUS_3            36              81
D1V9, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1            16              48
  CLUS_2            55              73
  CLUS_3            33              63
D1V10, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             2              12
  CLUS_2            18              67
  CLUS_3            84             105
D1V11, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             6              22
  CLUS_2            31              38
  CLUS_3            16              30
D1V12, multiclass
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  CLUS_1             9              25
  CLUS_2            36              37
  CLUS_3             8              28

Clustering(2) Variable = SV2C MUTATION ANALYSIS
D2V1, multiclass
D2V2, multiclass
D2V3, multiclass
        clus
vv       SV2C MUTATED SV2C WILD-TYPE
  CLUS_1            2             91
  CLUS_2            0            134
  CLUS_3            1             64
D2V4, multiclass
        clus
vv       SV2C MUTATED SV2C WILD-TYPE
  CLUS_1            0             71
  CLUS_2            0             83
  CLUS_3            3             42
D2V5, multiclass
D2V6, multiclass
        clus
vv       SV2C MUTATED SV2C WILD-TYPE
  CLUS_1            1            116
  CLUS_2            1            104
  CLUS_3            1             51
D2V7, multiclass
[1] "Remove cluster labels:" "SV2C MUTATED"          
clus
  SV2C MUTATED SV2C WILD-TYPE 
             2            278 
    TCGA-A3-3308     TCGA-A3-3311     TCGA-A3-3316     TCGA-A3-3317 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-A3-3319     TCGA-A3-3320     TCGA-A3-3322     TCGA-A3-3323 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-A3-3324     TCGA-A3-3326     TCGA-A3-3347     TCGA-A3-3349 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-A3-3351     TCGA-A3-3357     TCGA-A3-3358     TCGA-A3-3362 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-A3-3363     TCGA-A3-3365     TCGA-A3-3367     TCGA-A3-3370 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-A3-3372     TCGA-A3-3373     TCGA-A3-3376     TCGA-A3-3378 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-A3-3380     TCGA-A3-3382     TCGA-A3-3385     TCGA-A3-3387 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-AK-3429     TCGA-AK-3436     TCGA-AK-3444     TCGA-AK-3451 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-AK-3455     TCGA-AK-3456     TCGA-AK-3458     TCGA-B0-4700 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-4706     TCGA-B0-4712     TCGA-B0-4810     TCGA-B0-4811 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-4815     TCGA-B0-4816     TCGA-B0-4818     TCGA-B0-4823 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-4827     TCGA-B0-4852     TCGA-B0-4945     TCGA-B0-5075 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5077     TCGA-B0-5080     TCGA-B0-5081     TCGA-B0-5085 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5088     TCGA-B0-5092     TCGA-B0-5094     TCGA-B0-5095 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5096     TCGA-B0-5097     TCGA-B0-5099     TCGA-B0-5100 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5102     TCGA-B0-5104     TCGA-B0-5106     TCGA-B0-5107 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5108     TCGA-B0-5109     TCGA-B0-5110     TCGA-B0-5113 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5115     TCGA-B0-5116     TCGA-B0-5119     TCGA-B0-5120 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5121     TCGA-B0-5399     TCGA-B0-5400     TCGA-B0-5402 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5691     TCGA-B0-5692     TCGA-B0-5693     TCGA-B0-5694 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5695     TCGA-B0-5696     TCGA-B0-5697     TCGA-B0-5698 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5699     TCGA-B0-5701     TCGA-B0-5703     TCGA-B0-5705 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5706     TCGA-B0-5709     TCGA-B0-5710     TCGA-B0-5711 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5713     TCGA-B0-5812     TCGA-B2-3924     TCGA-B2-4098 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B2-4099     TCGA-B2-4101     TCGA-B2-4102     TCGA-B2-5633 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B2-5635     TCGA-B4-5377     TCGA-B8-4143     TCGA-B8-4146 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B8-4148     TCGA-B8-4151     TCGA-B8-4153     TCGA-B8-4154 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B8-4620     TCGA-B8-4621     TCGA-B8-4622     TCGA-B8-5158 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B8-5159     TCGA-B8-5163     TCGA-B8-5164     TCGA-B8-5165 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B8-5545     TCGA-B8-5546     TCGA-B8-5549     TCGA-B8-5551 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B8-5552     TCGA-BP-4161     TCGA-BP-4162     TCGA-BP-4163 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4164     TCGA-BP-4167     TCGA-BP-4770     TCGA-BP-4782 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4801     TCGA-BP-4960     TCGA-BP-4961     TCGA-BP-4962 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4963     TCGA-BP-4964     TCGA-BP-4967     TCGA-BP-4968 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4970     TCGA-BP-4971     TCGA-BP-4972     TCGA-BP-4973 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4974     TCGA-BP-4975     TCGA-BP-4976     TCGA-BP-4977 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4981     TCGA-BP-4982     TCGA-BP-4983     TCGA-BP-4985 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4986     TCGA-BP-4987     TCGA-BP-4988     TCGA-BP-4989 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4991     TCGA-BP-4992     TCGA-BP-4993     TCGA-BP-4995 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4998     TCGA-BP-4999     TCGA-BP-5000     TCGA-BP-5001 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5004     TCGA-BP-5006     TCGA-BP-5007     TCGA-BP-5008 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5009     TCGA-BP-5010     TCGA-BP-5168     TCGA-BP-5169 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5170     TCGA-BP-5173     TCGA-BP-5174     TCGA-BP-5175 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5176     TCGA-BP-5177     TCGA-BP-5178     TCGA-BP-5180 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5182     TCGA-BP-5183     TCGA-BP-5184     TCGA-BP-5186 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5187     TCGA-BP-5189     TCGA-BP-5190     TCGA-BP-5191 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5192     TCGA-BP-5194     TCGA-BP-5195     TCGA-BP-5196 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5198     TCGA-BP-5199     TCGA-BP-5200     TCGA-BP-5201 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5202     TCGA-CJ-4634     TCGA-CJ-4636     TCGA-CJ-4637 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-4638     TCGA-CJ-4639     TCGA-CJ-4640     TCGA-CJ-4641 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-4643     TCGA-CJ-4644     TCGA-CJ-4882     TCGA-CJ-4897 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-4899     TCGA-CJ-4901     TCGA-CJ-4902     TCGA-CJ-4903 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-4904     TCGA-CJ-4905     TCGA-CJ-4907     TCGA-CJ-4908 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-4912     TCGA-CJ-4916     TCGA-CJ-4918     TCGA-CJ-4920 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-4923     TCGA-CJ-5671     TCGA-CJ-5672     TCGA-CJ-5675 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-5676     TCGA-CJ-5677     TCGA-CJ-5678     TCGA-CJ-5679 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-5680     TCGA-CJ-5681     TCGA-CJ-5682     TCGA-CJ-5683 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-5684     TCGA-CJ-5686     TCGA-CJ-6027     TCGA-CJ-6028 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-6030     TCGA-CJ-6031     TCGA-CJ-6032     TCGA-CJ-6033 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CW-5580     TCGA-CW-5581     TCGA-CW-5583     TCGA-CW-5584 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CW-5585     TCGA-CW-5588     TCGA-CW-5589     TCGA-CW-5591 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CW-6087     TCGA-CW-6090     TCGA-CW-6093     TCGA-CZ-4853 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-4856     TCGA-CZ-4859     TCGA-CZ-4863     TCGA-CZ-4866 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5452     TCGA-CZ-5453     TCGA-CZ-5454     TCGA-CZ-5456 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5457     TCGA-CZ-5458     TCGA-CZ-5460     TCGA-CZ-5461 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5462     TCGA-CZ-5463     TCGA-CZ-5464     TCGA-CZ-5465 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5467     TCGA-CZ-5468     TCGA-CZ-5469     TCGA-CZ-5470 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5982     TCGA-CZ-5984     TCGA-CZ-5985     TCGA-CZ-5986 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5987     TCGA-CZ-5988     TCGA-CZ-5989     TCGA-EU-5904 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-EU-5905     TCGA-EU-5906 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" 
D2V8, multiclass
[1] "Remove cluster labels:" "SV2C MUTATED"          
clus
  SV2C MUTATED SV2C WILD-TYPE 
             2            278 
    TCGA-A3-3308     TCGA-A3-3311     TCGA-A3-3316     TCGA-A3-3317 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-A3-3319     TCGA-A3-3320     TCGA-A3-3322     TCGA-A3-3323 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-A3-3324     TCGA-A3-3326     TCGA-A3-3347     TCGA-A3-3349 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-A3-3351     TCGA-A3-3357     TCGA-A3-3358     TCGA-A3-3362 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-A3-3363     TCGA-A3-3365     TCGA-A3-3367     TCGA-A3-3370 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-A3-3372     TCGA-A3-3373     TCGA-A3-3376     TCGA-A3-3378 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-A3-3380     TCGA-A3-3382     TCGA-A3-3385     TCGA-A3-3387 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-AK-3429     TCGA-AK-3436     TCGA-AK-3444     TCGA-AK-3451 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-AK-3455     TCGA-AK-3456     TCGA-AK-3458     TCGA-B0-4700 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-4706     TCGA-B0-4712     TCGA-B0-4810     TCGA-B0-4811 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-4815     TCGA-B0-4816     TCGA-B0-4818     TCGA-B0-4823 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-4827     TCGA-B0-4852     TCGA-B0-4945     TCGA-B0-5075 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5077     TCGA-B0-5080     TCGA-B0-5081     TCGA-B0-5085 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5088     TCGA-B0-5092     TCGA-B0-5094     TCGA-B0-5095 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5096     TCGA-B0-5097     TCGA-B0-5099     TCGA-B0-5100 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5102     TCGA-B0-5104     TCGA-B0-5106     TCGA-B0-5107 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5108     TCGA-B0-5109     TCGA-B0-5110     TCGA-B0-5113 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5115     TCGA-B0-5116     TCGA-B0-5119     TCGA-B0-5120 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5121     TCGA-B0-5399     TCGA-B0-5400     TCGA-B0-5402 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5691     TCGA-B0-5692     TCGA-B0-5693     TCGA-B0-5694 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5695     TCGA-B0-5696     TCGA-B0-5697     TCGA-B0-5698 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5699     TCGA-B0-5701     TCGA-B0-5703     TCGA-B0-5705 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5706     TCGA-B0-5709     TCGA-B0-5710     TCGA-B0-5711 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5713     TCGA-B0-5812     TCGA-B2-3924     TCGA-B2-4098 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B2-4099     TCGA-B2-4101     TCGA-B2-4102     TCGA-B2-5633 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B2-5635     TCGA-B4-5377     TCGA-B8-4143     TCGA-B8-4146 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B8-4148     TCGA-B8-4151     TCGA-B8-4153     TCGA-B8-4154 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B8-4620     TCGA-B8-4621     TCGA-B8-4622     TCGA-B8-5158 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B8-5159     TCGA-B8-5163     TCGA-B8-5164     TCGA-B8-5165 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B8-5545     TCGA-B8-5546     TCGA-B8-5549     TCGA-B8-5551 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B8-5552     TCGA-BP-4161     TCGA-BP-4162     TCGA-BP-4163 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4164     TCGA-BP-4167     TCGA-BP-4770     TCGA-BP-4782 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4801     TCGA-BP-4960     TCGA-BP-4961     TCGA-BP-4962 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4963     TCGA-BP-4964     TCGA-BP-4967     TCGA-BP-4968 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4970     TCGA-BP-4971     TCGA-BP-4972     TCGA-BP-4973 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4974     TCGA-BP-4975     TCGA-BP-4976     TCGA-BP-4977 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4981     TCGA-BP-4982     TCGA-BP-4983     TCGA-BP-4985 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4986     TCGA-BP-4987     TCGA-BP-4988     TCGA-BP-4989 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4991     TCGA-BP-4992     TCGA-BP-4993     TCGA-BP-4995 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4998     TCGA-BP-4999     TCGA-BP-5000     TCGA-BP-5001 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5004     TCGA-BP-5006     TCGA-BP-5007     TCGA-BP-5008 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5009     TCGA-BP-5010     TCGA-BP-5168     TCGA-BP-5169 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5170     TCGA-BP-5173     TCGA-BP-5174     TCGA-BP-5175 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5176     TCGA-BP-5177     TCGA-BP-5178     TCGA-BP-5180 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5182     TCGA-BP-5183     TCGA-BP-5184     TCGA-BP-5186 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5187     TCGA-BP-5189     TCGA-BP-5190     TCGA-BP-5191 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5192     TCGA-BP-5194     TCGA-BP-5195     TCGA-BP-5196 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5198     TCGA-BP-5199     TCGA-BP-5200     TCGA-BP-5201 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5202     TCGA-CJ-4634     TCGA-CJ-4636     TCGA-CJ-4637 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-4638     TCGA-CJ-4639     TCGA-CJ-4640     TCGA-CJ-4641 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-4643     TCGA-CJ-4644     TCGA-CJ-4882     TCGA-CJ-4897 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-4899     TCGA-CJ-4901     TCGA-CJ-4902     TCGA-CJ-4903 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-4904     TCGA-CJ-4905     TCGA-CJ-4907     TCGA-CJ-4908 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-4912     TCGA-CJ-4916     TCGA-CJ-4918     TCGA-CJ-4920 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-4923     TCGA-CJ-5671     TCGA-CJ-5672     TCGA-CJ-5675 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-5676     TCGA-CJ-5677     TCGA-CJ-5678     TCGA-CJ-5679 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-5680     TCGA-CJ-5681     TCGA-CJ-5682     TCGA-CJ-5683 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-5684     TCGA-CJ-5686     TCGA-CJ-6027     TCGA-CJ-6028 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-6030     TCGA-CJ-6031     TCGA-CJ-6032     TCGA-CJ-6033 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CW-5580     TCGA-CW-5581     TCGA-CW-5583     TCGA-CW-5584 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CW-5585     TCGA-CW-5588     TCGA-CW-5589     TCGA-CW-5591 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CW-6087     TCGA-CW-6090     TCGA-CW-6093     TCGA-CZ-4853 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-4856     TCGA-CZ-4859     TCGA-CZ-4863     TCGA-CZ-4866 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5452     TCGA-CZ-5453     TCGA-CZ-5454     TCGA-CZ-5456 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5457     TCGA-CZ-5458     TCGA-CZ-5460     TCGA-CZ-5461 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5462     TCGA-CZ-5463     TCGA-CZ-5464     TCGA-CZ-5465 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5467     TCGA-CZ-5468     TCGA-CZ-5469     TCGA-CZ-5470 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5982     TCGA-CZ-5984     TCGA-CZ-5985     TCGA-CZ-5986 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5987     TCGA-CZ-5988     TCGA-CZ-5989     TCGA-EU-5904 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-EU-5905     TCGA-EU-5906 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" 
D2V9, multiclass
        clus
vv       SV2C MUTATED SV2C WILD-TYPE
  CLUS_1            1             63
  CLUS_2            0            128
  CLUS_3            2             94
D2V10, multiclass
        clus
vv       SV2C MUTATED SV2C WILD-TYPE
  CLUS_1            1             13
  CLUS_2            2             83
  CLUS_3            0            189
D2V11, multiclass
[1] "Remove cluster labels:" "SV2C MUTATED"          
clus
  SV2C MUTATED SV2C WILD-TYPE 
             2            141 
    TCGA-A3-3317     TCGA-A3-3358     TCGA-A3-3387     TCGA-AK-3458 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-4700     TCGA-B0-4706     TCGA-B0-4710     TCGA-B0-4712 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-4810     TCGA-B0-4811     TCGA-B0-4815     TCGA-B0-4816 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-4818     TCGA-B0-4852     TCGA-B0-5075     TCGA-B0-5080 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5085     TCGA-B0-5088     TCGA-B0-5399     TCGA-B0-5400 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5402     TCGA-B0-5691     TCGA-B0-5692     TCGA-B0-5693 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5694     TCGA-B0-5695     TCGA-B0-5696     TCGA-B0-5697 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5698     TCGA-B0-5699     TCGA-B0-5701     TCGA-B0-5703 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5705     TCGA-B0-5706     TCGA-B0-5707     TCGA-B0-5709 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5710     TCGA-B0-5711     TCGA-B0-5713     TCGA-B0-5812 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B2-5633     TCGA-B2-5635     TCGA-B4-5377     TCGA-B8-4146 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B8-4153     TCGA-B8-4621     TCGA-B8-5545     TCGA-B8-5546 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B8-5549     TCGA-B8-5551     TCGA-B8-5552     TCGA-BP-4770 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4960     TCGA-BP-4961     TCGA-BP-4967     TCGA-BP-4968 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4970     TCGA-BP-4971     TCGA-BP-4973     TCGA-BP-4974 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4975     TCGA-BP-4976     TCGA-BP-4977     TCGA-BP-4981 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4982     TCGA-BP-4985     TCGA-BP-4986     TCGA-BP-4987 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4988     TCGA-BP-4989     TCGA-BP-4992     TCGA-BP-4995 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4998     TCGA-BP-5000     TCGA-BP-5001     TCGA-BP-5007 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5008     TCGA-BP-5009     TCGA-CJ-4899     TCGA-CJ-5671 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-5672     TCGA-CJ-5675     TCGA-CJ-5676     TCGA-CJ-5677 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-5678     TCGA-CJ-5679     TCGA-CJ-5680     TCGA-CJ-5681 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-5682     TCGA-CJ-5683     TCGA-CJ-5684     TCGA-CJ-5686 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-6027     TCGA-CJ-6028     TCGA-CJ-6030     TCGA-CJ-6031 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-6032     TCGA-CJ-6033     TCGA-CW-5580     TCGA-CW-5581 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CW-5583     TCGA-CW-5584     TCGA-CW-5585     TCGA-CW-5588 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CW-5589     TCGA-CW-5591     TCGA-CW-6087     TCGA-CW-6090 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CW-6093     TCGA-CZ-4863     TCGA-CZ-4866     TCGA-CZ-5451 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5452     TCGA-CZ-5453     TCGA-CZ-5454     TCGA-CZ-5456 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5457     TCGA-CZ-5458     TCGA-CZ-5459     TCGA-CZ-5460 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5461     TCGA-CZ-5462     TCGA-CZ-5463     TCGA-CZ-5464 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5465     TCGA-CZ-5466     TCGA-CZ-5467     TCGA-CZ-5468 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5982     TCGA-CZ-5984 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5985     TCGA-CZ-5986     TCGA-CZ-5987     TCGA-CZ-5988 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5989     TCGA-EU-5904     TCGA-EU-5905     TCGA-EU-5906 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-EU-5907 
"SV2C WILD-TYPE" 
D2V12, multiclass
[1] "Remove cluster labels:" "SV2C MUTATED"          
clus
  SV2C MUTATED SV2C WILD-TYPE 
             2            141 
    TCGA-A3-3317     TCGA-A3-3358     TCGA-A3-3387     TCGA-AK-3458 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-4700     TCGA-B0-4706     TCGA-B0-4710     TCGA-B0-4712 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-4810     TCGA-B0-4811     TCGA-B0-4815     TCGA-B0-4816 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-4818     TCGA-B0-4852     TCGA-B0-5075     TCGA-B0-5080 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5085     TCGA-B0-5088     TCGA-B0-5399     TCGA-B0-5400 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5402     TCGA-B0-5691     TCGA-B0-5692     TCGA-B0-5693 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5694     TCGA-B0-5695     TCGA-B0-5696     TCGA-B0-5697 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5698     TCGA-B0-5699     TCGA-B0-5701     TCGA-B0-5703 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5705     TCGA-B0-5706     TCGA-B0-5707     TCGA-B0-5709 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B0-5710     TCGA-B0-5711     TCGA-B0-5713     TCGA-B0-5812 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B2-5633     TCGA-B2-5635     TCGA-B4-5377     TCGA-B8-4146 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B8-4153     TCGA-B8-4621     TCGA-B8-5545     TCGA-B8-5546 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-B8-5549     TCGA-B8-5551     TCGA-B8-5552     TCGA-BP-4770 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4960     TCGA-BP-4961     TCGA-BP-4967     TCGA-BP-4968 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4970     TCGA-BP-4971     TCGA-BP-4973     TCGA-BP-4974 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4975     TCGA-BP-4976     TCGA-BP-4977     TCGA-BP-4981 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4982     TCGA-BP-4985     TCGA-BP-4986     TCGA-BP-4987 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4988     TCGA-BP-4989     TCGA-BP-4992     TCGA-BP-4995 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-4998     TCGA-BP-5000     TCGA-BP-5001     TCGA-BP-5007 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-BP-5008     TCGA-BP-5009     TCGA-CJ-4899     TCGA-CJ-5671 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-5672     TCGA-CJ-5675     TCGA-CJ-5676     TCGA-CJ-5677 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-5678     TCGA-CJ-5679     TCGA-CJ-5680     TCGA-CJ-5681 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-5682     TCGA-CJ-5683     TCGA-CJ-5684     TCGA-CJ-5686 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-6027     TCGA-CJ-6028     TCGA-CJ-6030     TCGA-CJ-6031 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CJ-6032     TCGA-CJ-6033     TCGA-CW-5580     TCGA-CW-5581 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CW-5583     TCGA-CW-5584     TCGA-CW-5585     TCGA-CW-5588 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CW-5589     TCGA-CW-5591     TCGA-CW-6087     TCGA-CW-6090 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CW-6093     TCGA-CZ-4863     TCGA-CZ-4866     TCGA-CZ-5451 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5452     TCGA-CZ-5453     TCGA-CZ-5454     TCGA-CZ-5456 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5457     TCGA-CZ-5458     TCGA-CZ-5459     TCGA-CZ-5460 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5461     TCGA-CZ-5462     TCGA-CZ-5463     TCGA-CZ-5464 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5465     TCGA-CZ-5466     TCGA-CZ-5467     TCGA-CZ-5468 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5982     TCGA-CZ-5984 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5985     TCGA-CZ-5986     TCGA-CZ-5987     TCGA-CZ-5988 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-CZ-5989     TCGA-EU-5904     TCGA-EU-5905     TCGA-EU-5906 
"SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" "SV2C WILD-TYPE" 
    TCGA-EU-5907 
"SV2C WILD-TYPE" 

Clustering(3) Variable = VHL MUTATION ANALYSIS
D3V1, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          14            11
  CLUS_2           5            16
  CLUS_3           0             3
D3V2, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1           0             4
  CLUS_2          14            11
  CLUS_3           5            15
D3V3, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          48            45
  CLUS_2          61            73
  CLUS_3          29            36
D3V4, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          35            36
  CLUS_2          43            40
  CLUS_3          17            28
D3V5, multiclass
D3V6, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          60            57
  CLUS_2          44            61
  CLUS_3          27            25
D3V7, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          71            53
  CLUS_2          47            63
  CLUS_3          15            31
D3V8, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          11            20
  CLUS_2          72            60
  CLUS_3          50            67
D3V9, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          25            39
  CLUS_2          65            63
  CLUS_3          44            52
D3V10, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1           4            10
  CLUS_2          35            50
  CLUS_3          95            94
D3V11, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          11            17
  CLUS_2          30            39
  CLUS_3          24            22
D3V12, multiclass
        clus
vv       VHL MUTATED VHL WILD-TYPE
  CLUS_1          17            17
  CLUS_2          34            39
  CLUS_3          14            22

Clustering(4) Variable = BAP1 MUTATION ANALYSIS
D4V1, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            1             24
  CLUS_2            7             14
  CLUS_3            0              3
D4V2, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            0              4
  CLUS_2            1             24
  CLUS_3            7             13
D4V3, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1           12             81
  CLUS_2            8            126
  CLUS_3            7             58
D4V4, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            8             63
  CLUS_2            1             82
  CLUS_3            7             38
D4V5, multiclass
D4V6, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            8            109
  CLUS_2            9             96
  CLUS_3            5             47
D4V7, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            4            120
  CLUS_2           18             92
  CLUS_3            5             41
D4V8, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            1             30
  CLUS_2            1            131
  CLUS_3           25             92
D4V9, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            7             57
  CLUS_2            3            125
  CLUS_3           17             79
D4V10, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            5              9
  CLUS_2           16             69
  CLUS_3            6            183
D4V11, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            4             24
  CLUS_2            1             68
  CLUS_3            4             42
D4V12, multiclass
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  CLUS_1            4             30
  CLUS_2            1             72
  CLUS_3            4             32

Clustering(5) Variable = SETD2 MUTATION ANALYSIS
D5V1, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             2              23
  CLUS_2             3              18
  CLUS_3             0               3
D5V2, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             0               4
  CLUS_2             2              23
  CLUS_3             3              17
D5V3, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1            16              77
  CLUS_2            11             123
  CLUS_3             7              58
D5V4, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1            19              52
  CLUS_2             7              76
  CLUS_3             0              45
D5V5, multiclass
D5V6, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1            10             107
  CLUS_2            17              88
  CLUS_3             5              47
D5V7, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1            12             112
  CLUS_2            16              94
  CLUS_3             3              43
D5V8, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             2              29
  CLUS_2            14             118
  CLUS_3            15             102
D5V9, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             3              61
  CLUS_2            15             113
  CLUS_3            15              81
D5V10, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             0              14
  CLUS_2             9              76
  CLUS_3            24             165
D5V11, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             3              25
  CLUS_2            10              59
  CLUS_3             8              38
D5V12, multiclass
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  CLUS_1             5              29
  CLUS_2            13              60
  CLUS_3             3              33

Clustering(6) Variable = KDM5C MUTATION ANALYSIS
D6V1, multiclass
[1] "Remove cluster labels:" "KDM5C MUTATED"         
clus
  KDM5C MUTATED KDM5C WILD-TYPE 
              2              47 
     TCGA-A3-3308      TCGA-A3-3311      TCGA-A3-3316      TCGA-A3-3317 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A3-3320      TCGA-A3-3322      TCGA-A3-3324      TCGA-A3-3326 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A3-3346      TCGA-A3-3347      TCGA-A3-3349      TCGA-A3-3351 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A3-3362      TCGA-A3-3363      TCGA-A3-3365      TCGA-A3-3372 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A3-3378      TCGA-A3-3380      TCGA-A3-3382      TCGA-A3-3383 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-AK-3444      TCGA-AK-3455      TCGA-AK-3456      TCGA-AS-3778 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B2-3924      TCGA-B2-4098      TCGA-B2-4099      TCGA-B2-4102 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B8-4143      TCGA-B8-4148      TCGA-B8-4151      TCGA-B8-4154 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B8-4620      TCGA-BP-4161      TCGA-BP-4162      TCGA-BP-4163 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-BP-4164      TCGA-BP-4167      TCGA-CJ-4634      TCGA-CJ-4636 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CJ-4637      TCGA-CJ-4638      TCGA-CJ-4639      TCGA-CJ-4640 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CJ-4641      TCGA-CJ-4643      TCGA-CJ-4644 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
D6V2, multiclass
[1] "Remove cluster labels:" "KDM5C MUTATED"         
clus
  KDM5C MUTATED KDM5C WILD-TYPE 
              2              47 
     TCGA-A3-3308      TCGA-A3-3311      TCGA-A3-3316      TCGA-A3-3317 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A3-3320      TCGA-A3-3322      TCGA-A3-3324      TCGA-A3-3326 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A3-3346      TCGA-A3-3347      TCGA-A3-3349      TCGA-A3-3351 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A3-3362      TCGA-A3-3363      TCGA-A3-3365      TCGA-A3-3372 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A3-3378      TCGA-A3-3380      TCGA-A3-3382      TCGA-A3-3383 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-AK-3444      TCGA-AK-3455      TCGA-AK-3456      TCGA-AS-3778 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B2-3924      TCGA-B2-4098      TCGA-B2-4099      TCGA-B2-4102 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B8-4143      TCGA-B8-4148      TCGA-B8-4151      TCGA-B8-4154 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B8-4620      TCGA-BP-4161      TCGA-BP-4162      TCGA-BP-4163 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-BP-4164      TCGA-BP-4167      TCGA-CJ-4634      TCGA-CJ-4636 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CJ-4637      TCGA-CJ-4638      TCGA-CJ-4639      TCGA-CJ-4640 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CJ-4641      TCGA-CJ-4643      TCGA-CJ-4644 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
D6V3, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1             8              85
  CLUS_2             7             127
  CLUS_3             3              62
D6V4, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1             7              64
  CLUS_2             3              80
  CLUS_3             3              42
D6V5, multiclass
D6V6, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1             3             114
  CLUS_2            11              94
  CLUS_3             2              50
D6V7, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1             5             119
  CLUS_2            11              99
  CLUS_3             1              45
D6V8, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1             1              30
  CLUS_2             7             125
  CLUS_3             9             108
D6V9, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1             2              62
  CLUS_2             5             123
  CLUS_3            11              85
D6V10, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1             1              13
  CLUS_2             4              81
  CLUS_3            13             176
D6V11, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1             1              27
  CLUS_2             2              67
  CLUS_3             3              43
D6V12, multiclass
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  CLUS_1             2              32
  CLUS_2             2              71
  CLUS_3             2              34

Clustering(7) Variable = TP53 MUTATION ANALYSIS
D7V1, multiclass
[1] "Remove cluster labels:" "TP53 MUTATED"          
clus
  TP53 MUTATED TP53 WILD-TYPE 
             1             48 
    TCGA-A3-3311     TCGA-A3-3316     TCGA-A3-3317     TCGA-A3-3319 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A3-3320     TCGA-A3-3322     TCGA-A3-3323     TCGA-A3-3324 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A3-3326     TCGA-A3-3346     TCGA-A3-3347     TCGA-A3-3349 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A3-3351     TCGA-A3-3362     TCGA-A3-3363     TCGA-A3-3365 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A3-3372     TCGA-A3-3378     TCGA-A3-3380     TCGA-A3-3382 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A3-3383     TCGA-AK-3444     TCGA-AK-3455     TCGA-AK-3456 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-AS-3778     TCGA-B2-3924     TCGA-B2-4098     TCGA-B2-4099 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-B2-4102     TCGA-B8-4143     TCGA-B8-4148     TCGA-B8-4151 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-B8-4154     TCGA-B8-4620     TCGA-BP-4161     TCGA-BP-4162 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-BP-4163     TCGA-BP-4164     TCGA-BP-4167     TCGA-CJ-4634 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-CJ-4636     TCGA-CJ-4637     TCGA-CJ-4638     TCGA-CJ-4639 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-CJ-4640     TCGA-CJ-4641     TCGA-CJ-4643     TCGA-CJ-4644 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
D7V2, multiclass
[1] "Remove cluster labels:" "TP53 MUTATED"          
clus
  TP53 MUTATED TP53 WILD-TYPE 
             1             48 
    TCGA-A3-3311     TCGA-A3-3316     TCGA-A3-3317     TCGA-A3-3319 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A3-3320     TCGA-A3-3322     TCGA-A3-3323     TCGA-A3-3324 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A3-3326     TCGA-A3-3346     TCGA-A3-3347     TCGA-A3-3349 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A3-3351     TCGA-A3-3362     TCGA-A3-3363     TCGA-A3-3365 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A3-3372     TCGA-A3-3378     TCGA-A3-3380     TCGA-A3-3382 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-A3-3383     TCGA-AK-3444     TCGA-AK-3455     TCGA-AK-3456 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-AS-3778     TCGA-B2-3924     TCGA-B2-4098     TCGA-B2-4099 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-B2-4102     TCGA-B8-4143     TCGA-B8-4148     TCGA-B8-4151 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-B8-4154     TCGA-B8-4620     TCGA-BP-4161     TCGA-BP-4162 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-BP-4163     TCGA-BP-4164     TCGA-BP-4167     TCGA-CJ-4634 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-CJ-4636     TCGA-CJ-4637     TCGA-CJ-4638     TCGA-CJ-4639 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-CJ-4640     TCGA-CJ-4641     TCGA-CJ-4643     TCGA-CJ-4644 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
D7V3, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             92
  CLUS_2            2            132
  CLUS_3            3             62
D7V4, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3             68
  CLUS_2            1             82
  CLUS_3            1             44
D7V5, multiclass
D7V6, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            3            114
  CLUS_2            1            104
  CLUS_3            2             50
D7V7, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1            123
  CLUS_2            3            107
  CLUS_3            1             45
D7V8, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            0             31
  CLUS_2            1            131
  CLUS_3            4            113
D7V9, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            2             62
  CLUS_2            2            126
  CLUS_3            2             94
D7V10, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             13
  CLUS_2            3             82
  CLUS_3            2            187
D7V11, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             27
  CLUS_2            2             67
  CLUS_3            2             44
D7V12, multiclass
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  CLUS_1            1             33
  CLUS_2            2             71
  CLUS_3            2             34

Clustering(8) Variable = PTEN MUTATION ANALYSIS
D8V1, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             25
  CLUS_2            3             18
  CLUS_3            0              3
D8V2, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0              4
  CLUS_2            0             25
  CLUS_3            3             17
D8V3, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             89
  CLUS_2            3            131
  CLUS_3            2             63
D8V4, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            4             67
  CLUS_2            1             82
  CLUS_3            1             44
D8V5, multiclass
D8V6, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            5            112
  CLUS_2            2            103
  CLUS_3            2             50
D8V7, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0            124
  CLUS_2            7            103
  CLUS_3            1             45
D8V8, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             31
  CLUS_2            1            131
  CLUS_3            7            110
D8V9, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            3             61
  CLUS_2            2            126
  CLUS_3            4             92
D8V10, multiclass
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  CLUS_1            0             14
  CLUS_2            4             81
  CLUS_3            5            184
D8V11, multiclass
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             2            141 
    TCGA-A3-3317     TCGA-A3-3358     TCGA-A3-3387     TCGA-AK-3458 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-4700     TCGA-B0-4706     TCGA-B0-4710     TCGA-B0-4712 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-4811     TCGA-B0-4815     TCGA-B0-4816     TCGA-B0-4818 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-4852     TCGA-B0-5075     TCGA-B0-5080     TCGA-B0-5085 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-5088     TCGA-B0-5399     TCGA-B0-5400     TCGA-B0-5402 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-5691     TCGA-B0-5692     TCGA-B0-5693     TCGA-B0-5694 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-5695     TCGA-B0-5696     TCGA-B0-5697     TCGA-B0-5698 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-5699     TCGA-B0-5701     TCGA-B0-5702     TCGA-B0-5703 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-5705     TCGA-B0-5706     TCGA-B0-5707     TCGA-B0-5709 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-5710     TCGA-B0-5711     TCGA-B0-5713     TCGA-B0-5812 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B2-5633     TCGA-B2-5635     TCGA-B2-5641     TCGA-B4-5377 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B8-4146     TCGA-B8-4153     TCGA-B8-4621     TCGA-B8-5545 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B8-5546     TCGA-B8-5549     TCGA-B8-5551     TCGA-B8-5552 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-BP-4770     TCGA-BP-4960     TCGA-BP-4961     TCGA-BP-4967 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-BP-4968     TCGA-BP-4970     TCGA-BP-4971     TCGA-BP-4973 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-BP-4974     TCGA-BP-4975     TCGA-BP-4976     TCGA-BP-4977 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-BP-4981     TCGA-BP-4982     TCGA-BP-4985     TCGA-BP-4986 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-BP-4987     TCGA-BP-4988     TCGA-BP-4989     TCGA-BP-4992 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-BP-4995     TCGA-BP-4998     TCGA-BP-5000     TCGA-BP-5001 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-BP-5007     TCGA-BP-5008     TCGA-BP-5009     TCGA-CJ-4899 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CJ-5671     TCGA-CJ-5672     TCGA-CJ-5675     TCGA-CJ-5676 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CJ-5677     TCGA-CJ-5678     TCGA-CJ-5679     TCGA-CJ-5680 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CJ-5681     TCGA-CJ-5682     TCGA-CJ-5683     TCGA-CJ-5684 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CJ-5686     TCGA-CJ-6027     TCGA-CJ-6028     TCGA-CJ-6030 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CJ-6031     TCGA-CJ-6032     TCGA-CJ-6033     TCGA-CW-5580 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CW-5581     TCGA-CW-5583     TCGA-CW-5584     TCGA-CW-5585 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CW-5588     TCGA-CW-5589     TCGA-CW-5591     TCGA-CW-6087 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CW-6090     TCGA-CW-6093     TCGA-CZ-4863     TCGA-CZ-4866 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CZ-5451     TCGA-CZ-5452     TCGA-CZ-5453     TCGA-CZ-5454 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CZ-5456     TCGA-CZ-5457     TCGA-CZ-5458     TCGA-CZ-5459 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CZ-5460     TCGA-CZ-5461     TCGA-CZ-5462     TCGA-CZ-5463 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CZ-5464     TCGA-CZ-5465     TCGA-CZ-5466     TCGA-CZ-5467 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CZ-5468     TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5982 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CZ-5984     TCGA-CZ-5985     TCGA-CZ-5986     TCGA-CZ-5987 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CZ-5988     TCGA-CZ-5989     TCGA-EU-5904     TCGA-EU-5905 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-EU-5906 
"PTEN WILD-TYPE" 
D8V12, multiclass
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             2            141 
    TCGA-A3-3317     TCGA-A3-3358     TCGA-A3-3387     TCGA-AK-3458 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-4700     TCGA-B0-4706     TCGA-B0-4710     TCGA-B0-4712 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-4811     TCGA-B0-4815     TCGA-B0-4816     TCGA-B0-4818 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-4852     TCGA-B0-5075     TCGA-B0-5080     TCGA-B0-5085 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-5088     TCGA-B0-5399     TCGA-B0-5400     TCGA-B0-5402 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-5691     TCGA-B0-5692     TCGA-B0-5693     TCGA-B0-5694 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-5695     TCGA-B0-5696     TCGA-B0-5697     TCGA-B0-5698 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-5699     TCGA-B0-5701     TCGA-B0-5702     TCGA-B0-5703 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-5705     TCGA-B0-5706     TCGA-B0-5707     TCGA-B0-5709 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B0-5710     TCGA-B0-5711     TCGA-B0-5713     TCGA-B0-5812 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B2-5633     TCGA-B2-5635     TCGA-B2-5641     TCGA-B4-5377 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B8-4146     TCGA-B8-4153     TCGA-B8-4621     TCGA-B8-5545 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B8-5546     TCGA-B8-5549     TCGA-B8-5551     TCGA-B8-5552 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-BP-4770     TCGA-BP-4960     TCGA-BP-4961     TCGA-BP-4967 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-BP-4968     TCGA-BP-4970     TCGA-BP-4971     TCGA-BP-4973 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-BP-4974     TCGA-BP-4975     TCGA-BP-4976     TCGA-BP-4977 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-BP-4981     TCGA-BP-4982     TCGA-BP-4985     TCGA-BP-4986 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-BP-4987     TCGA-BP-4988     TCGA-BP-4989     TCGA-BP-4992 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-BP-4995     TCGA-BP-4998     TCGA-BP-5000     TCGA-BP-5001 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-BP-5007     TCGA-BP-5008     TCGA-BP-5009     TCGA-CJ-4899 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CJ-5671     TCGA-CJ-5672     TCGA-CJ-5675     TCGA-CJ-5676 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CJ-5677     TCGA-CJ-5678     TCGA-CJ-5679     TCGA-CJ-5680 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CJ-5681     TCGA-CJ-5682     TCGA-CJ-5683     TCGA-CJ-5684 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CJ-5686     TCGA-CJ-6027     TCGA-CJ-6028     TCGA-CJ-6030 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CJ-6031     TCGA-CJ-6032     TCGA-CJ-6033     TCGA-CW-5580 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CW-5581     TCGA-CW-5583     TCGA-CW-5584     TCGA-CW-5585 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CW-5588     TCGA-CW-5589     TCGA-CW-5591     TCGA-CW-6087 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CW-6090     TCGA-CW-6093     TCGA-CZ-4863     TCGA-CZ-4866 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CZ-5451     TCGA-CZ-5452     TCGA-CZ-5453     TCGA-CZ-5454 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CZ-5456     TCGA-CZ-5457     TCGA-CZ-5458     TCGA-CZ-5459 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CZ-5460     TCGA-CZ-5461     TCGA-CZ-5462     TCGA-CZ-5463 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CZ-5464     TCGA-CZ-5465     TCGA-CZ-5466     TCGA-CZ-5467 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CZ-5468     TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5982 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CZ-5984     TCGA-CZ-5985     TCGA-CZ-5986     TCGA-CZ-5987 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-CZ-5988     TCGA-CZ-5989     TCGA-EU-5904     TCGA-EU-5905 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-EU-5906 
"PTEN WILD-TYPE" 

Clustering(9) Variable = EBPL MUTATION ANALYSIS
D9V1, multiclass
[1] "Remove cluster labels:" "EBPL MUTATED"          
clus
  EBPL MUTATED EBPL WILD-TYPE 
             2             47 
    TCGA-A3-3308     TCGA-A3-3311     TCGA-A3-3316     TCGA-A3-3317 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-A3-3319     TCGA-A3-3320     TCGA-A3-3322     TCGA-A3-3323 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-A3-3324     TCGA-A3-3326     TCGA-A3-3346     TCGA-A3-3347 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-A3-3349     TCGA-A3-3351     TCGA-A3-3362     TCGA-A3-3363 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-A3-3365     TCGA-A3-3372     TCGA-A3-3378     TCGA-A3-3380 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-A3-3382     TCGA-A3-3383     TCGA-AK-3444     TCGA-AK-3455 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-AK-3456     TCGA-AS-3778     TCGA-B2-3924     TCGA-B2-4098 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-B2-4099     TCGA-B2-4102     TCGA-B8-4143     TCGA-B8-4148 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4620     TCGA-BP-4161 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-BP-4162     TCGA-BP-4163     TCGA-BP-4164     TCGA-BP-4167 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-CJ-4634     TCGA-CJ-4636     TCGA-CJ-4637     TCGA-CJ-4638 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-CJ-4640     TCGA-CJ-4641     TCGA-CJ-4644 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
D9V2, multiclass
[1] "Remove cluster labels:" "EBPL MUTATED"          
clus
  EBPL MUTATED EBPL WILD-TYPE 
             2             47 
    TCGA-A3-3308     TCGA-A3-3311     TCGA-A3-3316     TCGA-A3-3317 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-A3-3319     TCGA-A3-3320     TCGA-A3-3322     TCGA-A3-3323 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-A3-3324     TCGA-A3-3326     TCGA-A3-3346     TCGA-A3-3347 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-A3-3349     TCGA-A3-3351     TCGA-A3-3362     TCGA-A3-3363 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-A3-3365     TCGA-A3-3372     TCGA-A3-3378     TCGA-A3-3380 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-A3-3382     TCGA-A3-3383     TCGA-AK-3444     TCGA-AK-3455 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-AK-3456     TCGA-AS-3778     TCGA-B2-3924     TCGA-B2-4098 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-B2-4099     TCGA-B2-4102     TCGA-B8-4143     TCGA-B8-4148 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4620     TCGA-BP-4161 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-BP-4162     TCGA-BP-4163     TCGA-BP-4164     TCGA-BP-4167 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-CJ-4634     TCGA-CJ-4636     TCGA-CJ-4637     TCGA-CJ-4638 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
    TCGA-CJ-4640     TCGA-CJ-4641     TCGA-CJ-4644 
"EBPL WILD-TYPE" "EBPL WILD-TYPE" "EBPL WILD-TYPE" 
D9V3, multiclass
        clus
vv       EBPL MUTATED EBPL WILD-TYPE
  CLUS_1            0             93
  CLUS_2            4            130
  CLUS_3            2             63
D9V4, multiclass
        clus
vv       EBPL MUTATED EBPL WILD-TYPE
  CLUS_1            1             70
  CLUS_2            2             81
  CLUS_3            0             45
D9V5, multiclass
D9V6, multiclass
        clus
vv       EBPL MUTATED EBPL WILD-TYPE
  CLUS_1            1            116
  CLUS_2            3            102
  CLUS_3            0             52
D9V7, multiclass
        clus
vv       EBPL MUTATED EBPL WILD-TYPE
  CLUS_1            2            122
  CLUS_2            1            109
  CLUS_3            2             44
D9V8, multiclass
        clus
vv       EBPL MUTATED EBPL WILD-TYPE
  CLUS_1            2             29
  CLUS_2            2            130
  CLUS_3            1            116
D9V9, multiclass
        clus
vv       EBPL MUTATED EBPL WILD-TYPE
  CLUS_1            0             64
  CLUS_2            5            123
  CLUS_3            1             95
D9V10, multiclass
        clus
vv       EBPL MUTATED EBPL WILD-TYPE
  CLUS_1            0             14
  CLUS_2            0             85
  CLUS_3            6            183
D9V11, multiclass
        clus
vv       EBPL MUTATED EBPL WILD-TYPE
  CLUS_1            0             28
  CLUS_2            3             66
  CLUS_3            1             45
D9V12, multiclass
        clus
vv       EBPL MUTATED EBPL WILD-TYPE
  CLUS_1            1             33
  CLUS_2            3             70
  CLUS_3            0             36

Clustering(10) Variable = TOR1A MUTATION ANALYSIS
D10V1, multiclass
[1] "Remove cluster labels:" "TOR1A MUTATED"         
clus
  TOR1A MUTATED TOR1A WILD-TYPE 
              1              48 
     TCGA-A3-3308      TCGA-A3-3311      TCGA-A3-3316      TCGA-A3-3317 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-A3-3319      TCGA-A3-3320      TCGA-A3-3322      TCGA-A3-3323 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-A3-3324      TCGA-A3-3326      TCGA-A3-3346      TCGA-A3-3347 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-A3-3349      TCGA-A3-3351      TCGA-A3-3362      TCGA-A3-3363 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-A3-3372      TCGA-A3-3378      TCGA-A3-3380      TCGA-A3-3382 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-A3-3383      TCGA-AK-3444      TCGA-AK-3455      TCGA-AK-3456 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-AS-3778      TCGA-B2-3924      TCGA-B2-4098      TCGA-B2-4099 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B2-4102      TCGA-B8-4143      TCGA-B8-4148      TCGA-B8-4151 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B8-4154      TCGA-B8-4620      TCGA-BP-4161      TCGA-BP-4162 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-BP-4163      TCGA-BP-4164      TCGA-BP-4167      TCGA-CJ-4634 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CJ-4636      TCGA-CJ-4637      TCGA-CJ-4638      TCGA-CJ-4639 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CJ-4640      TCGA-CJ-4641      TCGA-CJ-4643      TCGA-CJ-4644 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
D10V2, multiclass
[1] "Remove cluster labels:" "TOR1A MUTATED"         
clus
  TOR1A MUTATED TOR1A WILD-TYPE 
              1              48 
     TCGA-A3-3308      TCGA-A3-3311      TCGA-A3-3316      TCGA-A3-3317 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-A3-3319      TCGA-A3-3320      TCGA-A3-3322      TCGA-A3-3323 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-A3-3324      TCGA-A3-3326      TCGA-A3-3346      TCGA-A3-3347 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-A3-3349      TCGA-A3-3351      TCGA-A3-3362      TCGA-A3-3363 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-A3-3372      TCGA-A3-3378      TCGA-A3-3380      TCGA-A3-3382 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-A3-3383      TCGA-AK-3444      TCGA-AK-3455      TCGA-AK-3456 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-AS-3778      TCGA-B2-3924      TCGA-B2-4098      TCGA-B2-4099 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B2-4102      TCGA-B8-4143      TCGA-B8-4148      TCGA-B8-4151 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B8-4154      TCGA-B8-4620      TCGA-BP-4161      TCGA-BP-4162 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-BP-4163      TCGA-BP-4164      TCGA-BP-4167      TCGA-CJ-4634 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CJ-4636      TCGA-CJ-4637      TCGA-CJ-4638      TCGA-CJ-4639 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CJ-4640      TCGA-CJ-4641      TCGA-CJ-4643      TCGA-CJ-4644 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
D10V3, multiclass
        clus
vv       TOR1A MUTATED TOR1A WILD-TYPE
  CLUS_1             1              92
  CLUS_2             2             132
  CLUS_3             0              65
D10V4, multiclass
[1] "Remove cluster labels:" "TOR1A MUTATED"         
clus
  TOR1A MUTATED TOR1A WILD-TYPE 
              2             197 
     TCGA-A3-3357      TCGA-A3-3358      TCGA-A3-3367      TCGA-A3-3370 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-A3-3373      TCGA-A3-3376      TCGA-A3-3385      TCGA-A3-3387 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-AK-3458      TCGA-B0-4700      TCGA-B0-4706      TCGA-B0-4710 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B0-4712      TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4815 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B0-4816      TCGA-B0-4818      TCGA-B0-4823      TCGA-B0-4827 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B0-4842      TCGA-B0-4852      TCGA-B0-4945      TCGA-B0-5080 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B0-5092      TCGA-B0-5094      TCGA-B0-5095      TCGA-B0-5097 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B0-5099      TCGA-B0-5100      TCGA-B0-5102      TCGA-B0-5104 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B0-5106      TCGA-B0-5107      TCGA-B0-5108      TCGA-B0-5109 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B0-5110      TCGA-B0-5113      TCGA-B0-5115      TCGA-B0-5116 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B0-5119      TCGA-B0-5120      TCGA-B0-5121      TCGA-B0-5399 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B0-5400      TCGA-B0-5402      TCGA-B0-5691      TCGA-B0-5692 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B0-5693      TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5696 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B0-5697      TCGA-B0-5698      TCGA-B0-5699      TCGA-B0-5701 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B0-5702      TCGA-B0-5703      TCGA-B0-5705      TCGA-B0-5706 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B0-5707      TCGA-B0-5709      TCGA-B0-5710      TCGA-B0-5711 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B0-5713      TCGA-B0-5812      TCGA-B2-4101      TCGA-B2-5633 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B2-5635      TCGA-B2-5641      TCGA-B4-5377      TCGA-B8-4146 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B8-4153      TCGA-B8-4621      TCGA-B8-4622      TCGA-B8-5158 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B8-5159      TCGA-B8-5163      TCGA-B8-5164      TCGA-B8-5165 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B8-5545      TCGA-B8-5546      TCGA-B8-5549      TCGA-B8-5551 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-B8-5552      TCGA-BP-4770      TCGA-BP-4782      TCGA-BP-4801 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-BP-4993      TCGA-BP-5010      TCGA-BP-5169      TCGA-BP-5170 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-BP-5173      TCGA-BP-5174      TCGA-BP-5175      TCGA-BP-5176 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-BP-5177      TCGA-BP-5178      TCGA-BP-5180      TCGA-BP-5182 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-BP-5183      TCGA-BP-5184      TCGA-BP-5185      TCGA-BP-5186 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-BP-5187      TCGA-BP-5189      TCGA-BP-5190      TCGA-BP-5191 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-BP-5192      TCGA-BP-5194      TCGA-BP-5195      TCGA-BP-5196 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-BP-5198      TCGA-BP-5199      TCGA-BP-5200      TCGA-BP-5201 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-BP-5202      TCGA-CJ-4882      TCGA-CJ-4897      TCGA-CJ-4901 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CJ-4902      TCGA-CJ-4903      TCGA-CJ-4904      TCGA-CJ-4905 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CJ-4907      TCGA-CJ-4908      TCGA-CJ-4912      TCGA-CJ-4913 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CJ-4916      TCGA-CJ-4918      TCGA-CJ-4920      TCGA-CJ-4923 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CJ-5671      TCGA-CJ-5672      TCGA-CJ-5675      TCGA-CJ-5676 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CJ-5677      TCGA-CJ-5678      TCGA-CJ-5679      TCGA-CJ-5680 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CJ-5681      TCGA-CJ-5682      TCGA-CJ-5683      TCGA-CJ-5684 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CJ-5686      TCGA-CJ-6027      TCGA-CJ-6028      TCGA-CJ-6030 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CJ-6031      TCGA-CJ-6032      TCGA-CJ-6033      TCGA-CW-5580 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CW-5581      TCGA-CW-5583      TCGA-CW-5584      TCGA-CW-5585 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CW-5588      TCGA-CW-5589      TCGA-CW-5591      TCGA-CW-6087 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CW-6090      TCGA-CW-6093      TCGA-CZ-4853      TCGA-CZ-4856 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CZ-4859      TCGA-CZ-4863      TCGA-CZ-4866      TCGA-CZ-5451 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CZ-5452      TCGA-CZ-5453      TCGA-CZ-5454      TCGA-CZ-5456 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5459      TCGA-CZ-5460 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CZ-5461      TCGA-CZ-5462      TCGA-CZ-5463      TCGA-CZ-5464 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CZ-5465      TCGA-CZ-5466      TCGA-CZ-5467      TCGA-CZ-5468 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5982      TCGA-CZ-5984 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CZ-5985      TCGA-CZ-5986      TCGA-CZ-5987      TCGA-CZ-5988 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-CZ-5989      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906 
"TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" "TOR1A WILD-TYPE" 
     TCGA-EU-5907 
"TOR1A WILD-TYPE" 
D10V5, multiclass
D10V6, multiclass
        clus
vv       TOR1A MUTATED TOR1A WILD-TYPE
  CLUS_1             3             114
  CLUS_2             0             105
  CLUS_3             0              52
D10V7, multiclass
        clus
vv       TOR1A MUTATED TOR1A WILD-TYPE
  CLUS_1             1             123
  CLUS_2             1             109
  CLUS_3             1              45
D10V8, multiclass
        clus
vv       TOR1A MUTATED TOR1A WILD-TYPE
  CLUS_1             0              31
  CLUS_2             2             130
  CLUS_3             1             116
D10V9, multiclass
        clus
vv       TOR1A MUTATED TOR1A WILD-TYPE
  CLUS_1             0              64
  CLUS_2             2             126
  CLUS_3             1              95
D10V10, multiclass
        clus
vv       TOR1A MUTATED TOR1A WILD-TYPE
  CLUS_1             0              14
  CLUS_2             1              84
  CLUS_3             2             187
D10V11, multiclass
D10V12, multiclass
                           V1                            V2 
                  "MRNA_CNMF"          "MRNA_CHIERARCHICAL" 
                           V3                            V4 
                    "CN_CNMF"            "METHLYATION_CNMF" 
                           V5                            V6 
                  "RPPA_CNMF"          "RPPA_CHIERARCHICAL" 
                           V7                            V8 
               "MRNASEQ_CNMF"       "MRNASEQ_CHIERARCHICAL" 
                           V9                           V10 
                "MIRSEQ_CNMF"        "MIRSEQ_CHIERARCHICAL" 
                          V11                           V12 
         "MIRSEQ_MATURE_CNMF" "MIRSEQ_MATURE_CHIERARCHICAL" 
> q(save="no")
