
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/423600/KIRP-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/KIRP-TP/3536999/KIRP-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=0.05", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KIRP-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=KIRP-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=127, in cluster file=111, common to both=111
[1]   5 111
[1] "IL32 MUTATION ANALYSIS"
[1] 3
  IL32 MUTATED IL32 WILD-TYPE 
             4            107 
  IL32 MUTATED IL32 WILD-TYPE 
             4            107 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              4             107 
  CDC27 MUTATED CDC27 WILD-TYPE 
              4             107 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
            7           104 
  NF2 MUTATED NF2 WILD-TYPE 
            7           104 
[1] "PPARGC1B MUTATION ANALYSIS"
[1] 3
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 3                108 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 3                108 
[1] "SFRS2IP MUTATION ANALYSIS"
[1] 3
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
                5               106 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
                5               106 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 8 rows and 111 columns.

Variable 1:'CN_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
[5] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[7] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 111 columns, 0 survival variables, and 8 non-survival variables.
CN_CNMF, nv=5, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, 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=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, 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 = IL32 MUTATION ANALYSIS
D1V1, multiclass
D1V2, multiclass
[1] "Remove cluster labels:" "IL32 MUTATED"          
clus
  IL32 MUTATED IL32 WILD-TYPE 
             2             94 
    TCGA-A4-7286     TCGA-A4-7287     TCGA-A4-7288     TCGA-A4-7583 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-7584     TCGA-A4-7585     TCGA-A4-7732     TCGA-A4-7734 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-7828     TCGA-A4-7915     TCGA-A4-7996     TCGA-A4-7997 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-8098     TCGA-A4-8310     TCGA-A4-8311     TCGA-A4-8312 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-8516     TCGA-A4-8630     TCGA-AL-7173     TCGA-B1-5398 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B3-8121     TCGA-B9-5155     TCGA-B9-5156     TCGA-B9-7268 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5875     TCGA-BQ-5876     TCGA-BQ-5877     TCGA-BQ-5878 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5881     TCGA-BQ-5882 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5883     TCGA-BQ-5884     TCGA-BQ-5885     TCGA-BQ-5886 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5887     TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5891     TCGA-BQ-5892     TCGA-BQ-5894     TCGA-BQ-7044 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7045     TCGA-BQ-7046     TCGA-BQ-7048     TCGA-BQ-7049 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7053     TCGA-BQ-7055 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7056     TCGA-BQ-7058     TCGA-BQ-7059     TCGA-BQ-7060 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7061     TCGA-BQ-7062     TCGA-DW-5560     TCGA-DW-5561 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-7834     TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-7841     TCGA-DW-7842     TCGA-DZ-6131     TCGA-DZ-6132 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DZ-6133     TCGA-DZ-6134     TCGA-DZ-6135     TCGA-EV-5901 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-G7-6789     TCGA-G7-6790 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502     TCGA-GL-6846 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-7966     TCGA-GL-8500     TCGA-HE-7128 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-HE-7129     TCGA-HE-7130     TCGA-IZ-8195     TCGA-IZ-8196 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-J7-6720     TCGA-J7-8537 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" 
D1V3, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            2             24
  CLUS_2            1             23
  CLUS_3            0             25
D1V4, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            1             17
  CLUS_2            2             34
  CLUS_3            0             21
D1V5, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            1             30
  CLUS_2            0             40
  CLUS_3            2             21
  CLUS_4            1             16
D1V6, multiclass
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  CLUS_1            1             39
  CLUS_2            2             29
  CLUS_3            0             11
  CLUS_4            1             28
D1V7, multiclass
[1] "Remove cluster labels:" "IL32 MUTATED"          
clus
  IL32 MUTATED IL32 WILD-TYPE 
             2             94 
    TCGA-A4-7286     TCGA-A4-7287     TCGA-A4-7288     TCGA-A4-7583 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-7584     TCGA-A4-7585     TCGA-A4-7732     TCGA-A4-7734 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-7828     TCGA-A4-7915     TCGA-A4-7996     TCGA-A4-7997 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-8098     TCGA-A4-8310     TCGA-A4-8311     TCGA-A4-8312 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-8516     TCGA-A4-8630     TCGA-AL-7173     TCGA-B1-5398 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B3-8121     TCGA-B9-5155     TCGA-B9-5156     TCGA-B9-7268 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5875     TCGA-BQ-5876     TCGA-BQ-5877     TCGA-BQ-5878 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5881     TCGA-BQ-5882 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5883     TCGA-BQ-5884     TCGA-BQ-5885     TCGA-BQ-5886 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5887     TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5891     TCGA-BQ-5892     TCGA-BQ-5894     TCGA-BQ-7044 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7045     TCGA-BQ-7046     TCGA-BQ-7048     TCGA-BQ-7049 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7053     TCGA-BQ-7055 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7056     TCGA-BQ-7058     TCGA-BQ-7059     TCGA-BQ-7060 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7061     TCGA-BQ-7062     TCGA-DW-5560     TCGA-DW-5561 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-7834     TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-7841     TCGA-DW-7842     TCGA-DZ-6131     TCGA-DZ-6132 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DZ-6133     TCGA-DZ-6134     TCGA-DZ-6135     TCGA-EV-5901 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-G7-6789     TCGA-G7-6790 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502     TCGA-GL-6846 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-7966     TCGA-GL-8500     TCGA-HE-7128 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-HE-7129     TCGA-HE-7130     TCGA-IZ-8195     TCGA-IZ-8196 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-J7-6720     TCGA-J7-8537 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" 
D1V8, multiclass
[1] "Remove cluster labels:" "IL32 MUTATED"          
clus
  IL32 MUTATED IL32 WILD-TYPE 
             2             94 
    TCGA-A4-7286     TCGA-A4-7287     TCGA-A4-7288     TCGA-A4-7583 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-7584     TCGA-A4-7585     TCGA-A4-7732     TCGA-A4-7734 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-7828     TCGA-A4-7915     TCGA-A4-7996     TCGA-A4-7997 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-8098     TCGA-A4-8310     TCGA-A4-8311     TCGA-A4-8312 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-8516     TCGA-A4-8630     TCGA-AL-7173     TCGA-B1-5398 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B3-8121     TCGA-B9-5155     TCGA-B9-5156     TCGA-B9-7268 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5875     TCGA-BQ-5876     TCGA-BQ-5877     TCGA-BQ-5878 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5881     TCGA-BQ-5882 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5883     TCGA-BQ-5884     TCGA-BQ-5885     TCGA-BQ-5886 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5887     TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5891     TCGA-BQ-5892     TCGA-BQ-5894     TCGA-BQ-7044 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7045     TCGA-BQ-7046     TCGA-BQ-7048     TCGA-BQ-7049 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7053     TCGA-BQ-7055 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7056     TCGA-BQ-7058     TCGA-BQ-7059     TCGA-BQ-7060 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7061     TCGA-BQ-7062     TCGA-DW-5560     TCGA-DW-5561 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-7834     TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-7841     TCGA-DW-7842     TCGA-DZ-6131     TCGA-DZ-6132 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DZ-6133     TCGA-DZ-6134     TCGA-DZ-6135     TCGA-EV-5901 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-G7-6789     TCGA-G7-6790 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502     TCGA-GL-6846 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-7966     TCGA-GL-8500     TCGA-HE-7128 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-HE-7129     TCGA-HE-7130     TCGA-IZ-8195     TCGA-IZ-8196 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-J7-6720     TCGA-J7-8537 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" 

Clustering(2) Variable = CDC27 MUTATION ANALYSIS
D2V1, multiclass
D2V2, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             0              23
  CLUS_2             2              43
  CLUS_3             2              26
D2V3, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1              25
  CLUS_2             1              23
  CLUS_3             2              23
D2V4, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1              17
  CLUS_2             2              34
  CLUS_3             1              20
D2V5, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             0              31
  CLUS_2             1              39
  CLUS_3             2              21
  CLUS_4             1              16
D2V6, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1              39
  CLUS_2             2              29
  CLUS_3             1              10
  CLUS_4             0              29
D2V7, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             2              31
  CLUS_2             1              36
  CLUS_3             1              25
D2V8, multiclass
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  CLUS_1             1              40
  CLUS_2             2              13
  CLUS_3             1              39

Clustering(3) Variable = NF2 MUTATION ANALYSIS
D3V1, multiclass
D3V2, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           0            23
  CLUS_2           2            43
  CLUS_3           5            23
D3V3, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           2            24
  CLUS_2           3            21
  CLUS_3           0            25
D3V4, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           3            15
  CLUS_2           2            34
  CLUS_3           0            21
D3V5, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           2            29
  CLUS_2           2            38
  CLUS_3           1            22
  CLUS_4           2            15
D3V6, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           2            38
  CLUS_2           3            28
  CLUS_3           0            11
  CLUS_4           2            27
D3V7, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           2            31
  CLUS_2           3            34
  CLUS_3           2            24
D3V8, multiclass
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  CLUS_1           2            39
  CLUS_2           3            12
  CLUS_3           2            38

Clustering(4) Variable = PPARGC1B MUTATION ANALYSIS
D4V1, multiclass
D4V2, multiclass
[1] "Remove cluster labels:" "PPARGC1B MUTATED"      
clus
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 1                 95 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7584         TCGA-A4-7585 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7732         TCGA-A4-7734         TCGA-A4-7828 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-7996         TCGA-A4-7997 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-8312         TCGA-A4-8630         TCGA-AL-7173 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-8121         TCGA-B9-5155 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-5156         TCGA-B9-7268         TCGA-BQ-5875 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7837         TCGA-DW-7838 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7842         TCGA-DZ-6131         TCGA-DZ-6132 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7773         TCGA-GL-7966 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-GL-8500         TCGA-HE-7128         TCGA-HE-7129 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-HE-7130         TCGA-IZ-8195         TCGA-IZ-8196 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
D4V3, multiclass
[1] "Remove cluster labels:" "PPARGC1B MUTATED"      
clus
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 2                 73 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3472         TCGA-AL-3473 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B3-4104         TCGA-B9-4113         TCGA-B9-4114 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4617 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5876         TCGA-BQ-5877 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7056         TCGA-BQ-7058 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-GL-7966         TCGA-HE-7128         TCGA-HE-7129 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-HE-7130 
"PPARGC1B WILD-TYPE" 
D4V4, multiclass
[1] "Remove cluster labels:" "PPARGC1B MUTATED"      
clus
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 2                 73 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3472         TCGA-AL-3473 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B3-4104         TCGA-B9-4113         TCGA-B9-4114 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4617 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5876         TCGA-BQ-5877 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7056         TCGA-BQ-7058 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-GL-7966         TCGA-HE-7128         TCGA-HE-7129 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-HE-7130 
"PPARGC1B WILD-TYPE" 
D4V5, multiclass
        clus
vv       PPARGC1B MUTATED PPARGC1B WILD-TYPE
  CLUS_1                2                 29
  CLUS_2                0                 40
  CLUS_3                0                 23
  CLUS_4                1                 16
D4V6, multiclass
        clus
vv       PPARGC1B MUTATED PPARGC1B WILD-TYPE
  CLUS_1                0                 40
  CLUS_2                0                 31
  CLUS_3                0                 11
  CLUS_4                3                 26
D4V7, multiclass
[1] "Remove cluster labels:" "PPARGC1B MUTATED"      
clus
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 1                 95 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7584         TCGA-A4-7585 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7732         TCGA-A4-7734         TCGA-A4-7828 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-7996         TCGA-A4-7997 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-8312         TCGA-A4-8630         TCGA-AL-7173 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-8121         TCGA-B9-5155 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-5156         TCGA-B9-7268         TCGA-BQ-5875 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7837         TCGA-DW-7838 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7842         TCGA-DZ-6131         TCGA-DZ-6132 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7773         TCGA-GL-7966 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-GL-8500         TCGA-HE-7128         TCGA-HE-7129 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-HE-7130         TCGA-IZ-8195         TCGA-IZ-8196 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
D4V8, multiclass
[1] "Remove cluster labels:" "PPARGC1B MUTATED"      
clus
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 1                 95 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7584         TCGA-A4-7585 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7732         TCGA-A4-7734         TCGA-A4-7828 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-7996         TCGA-A4-7997 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-8312         TCGA-A4-8630         TCGA-AL-7173 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-8121         TCGA-B9-5155 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-5156         TCGA-B9-7268         TCGA-BQ-5875 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7837         TCGA-DW-7838 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7842         TCGA-DZ-6131         TCGA-DZ-6132 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7773         TCGA-GL-7966 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-GL-8500         TCGA-HE-7128         TCGA-HE-7129 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-HE-7130         TCGA-IZ-8195         TCGA-IZ-8196 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 

Clustering(5) Variable = SFRS2IP MUTATION ANALYSIS
D5V1, multiclass
D5V2, multiclass
        clus
vv       SFRS2IP MUTATED SFRS2IP WILD-TYPE
  CLUS_1               2                21
  CLUS_2               1                44
  CLUS_3               2                26
D5V3, multiclass
        clus
vv       SFRS2IP MUTATED SFRS2IP WILD-TYPE
  CLUS_1               1                25
  CLUS_2               3                21
  CLUS_3               0                25
D5V4, multiclass
        clus
vv       SFRS2IP MUTATED SFRS2IP WILD-TYPE
  CLUS_1               1                17
  CLUS_2               1                35
  CLUS_3               2                19
D5V5, multiclass
        clus
vv       SFRS2IP MUTATED SFRS2IP WILD-TYPE
  CLUS_1               1                30
  CLUS_2               3                37
  CLUS_3               0                23
  CLUS_4               1                16
D5V6, multiclass
        clus
vv       SFRS2IP MUTATED SFRS2IP WILD-TYPE
  CLUS_1               3                37
  CLUS_2               1                30
  CLUS_3               0                11
  CLUS_4               1                28
D5V7, multiclass
        clus
vv       SFRS2IP MUTATED SFRS2IP WILD-TYPE
  CLUS_1               2                31
  CLUS_2               2                35
  CLUS_3               1                25
D5V8, multiclass
        clus
vv       SFRS2IP MUTATED SFRS2IP WILD-TYPE
  CLUS_1               1                40
  CLUS_2               1                14
  CLUS_3               3                37
                           V1                            V2 
                    "CN_CNMF"            "METHLYATION_CNMF" 
                           V3                            V4 
               "MRNASEQ_CNMF"       "MRNASEQ_CHIERARCHICAL" 
                           V5                            V6 
                "MIRSEQ_CNMF"        "MIRSEQ_CHIERARCHICAL" 
                           V7                            V8 
         "MIRSEQ_MATURE_CNMF" "MIRSEQ_MATURE_CHIERARCHICAL" 
> q(save="no")
