
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_cnvarms_onlysig.2.4053/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Cluster_cnvarms_onlysig.2.4053/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/335538/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/PRAD-TP/2667029/1.GDAC_mergedClustering.Finished/PRAD-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=PRAD-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=PRAD-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=178, in cluster file=177, common to both=177
[1] "Reduce the number of clustering variables from 80 to 26."
[1]  26 177
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4               173 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4               173 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4               173 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4               173 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                6               171 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                6               171 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               15               162 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               15               162 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               12               165 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               12               165 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                8               169 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                8               169 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               17               160 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               17               160 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                5               172 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                5               172 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                174 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                174 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                174 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                174 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                174 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                174 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3               174 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3               174 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7               170 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7               170 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               46               131 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               46               131 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               173 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               173 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                171 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                171 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                172 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                172 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 9                168 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 9                168 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                12                165 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                12                165 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                22                155 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                22                155 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                18                159 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                18                159 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                19                158 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                19                158 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                24                153 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                24                153 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                173 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                173 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 4                173 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 4                173 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 6                171 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 6                171 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 6 rows and 177 columns.

Variable 1:'CN_CNMF':	nDistinctValues=4,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 177 columns, 0 survival variables, and 6 non-survival variables.
CN_CNMF, nv=4, 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=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1q gain mutation analysis
D1V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                39
  CLUS_2               1                82
  CLUS_3               3                51
  CLUS_4               0                 1
D1V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                51
  CLUS_2               0                50
  CLUS_3               2                66
D1V3, multiclass
[1] "Remove cluster labels:" "1Q GAIN MUTATED"       
clus
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                2               138 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5744        TCGA-CH-5746        TCGA-CH-5748 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752        TCGA-CH-5753 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5754        TCGA-CH-5762        TCGA-CH-5763        TCGA-CH-5764 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772        TCGA-CH-5788 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791        TCGA-CH-5792 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495        TCGA-EJ-5496 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5507        TCGA-EJ-5508 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542        TCGA-EJ-7115 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7785 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FC-7708        TCGA-G9-6332        TCGA-G9-6336        TCGA-G9-6348 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6378        TCGA-G9-6384 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-7510        TCGA-G9-7519 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-7521        TCGA-G9-7522        TCGA-G9-7523        TCGA-G9-7525 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7078        TCGA-HC-7209        TCGA-HC-7210 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HC-7738        TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749        TCGA-HC-7750 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819        TCGA-HC-7820 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HC-7821        TCGA-HC-8256        TCGA-HC-8257        TCGA-HC-8258 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HC-8259        TCGA-HC-8260        TCGA-HC-8261        TCGA-HC-8262 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HC-8265        TCGA-HC-8266        TCGA-HI-7168        TCGA-HI-7169 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HI-7171        TCGA-J4-8198 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
D1V4, multiclass
[1] "Remove cluster labels:" "1Q GAIN MUTATED"       
clus
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                2               138 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5744        TCGA-CH-5746        TCGA-CH-5748 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752        TCGA-CH-5753 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5754        TCGA-CH-5762        TCGA-CH-5763        TCGA-CH-5764 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772        TCGA-CH-5788 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791        TCGA-CH-5792 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495        TCGA-EJ-5496 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5507        TCGA-EJ-5508 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542        TCGA-EJ-7115 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7785 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FC-7708        TCGA-G9-6332        TCGA-G9-6336        TCGA-G9-6348 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6378        TCGA-G9-6384 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-7510        TCGA-G9-7519 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-7521        TCGA-G9-7522        TCGA-G9-7523        TCGA-G9-7525 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7078        TCGA-HC-7209        TCGA-HC-7210 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HC-7738        TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749        TCGA-HC-7750 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819        TCGA-HC-7820 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HC-7821        TCGA-HC-8256        TCGA-HC-8257        TCGA-HC-8258 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HC-8259        TCGA-HC-8260        TCGA-HC-8261        TCGA-HC-8262 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HC-8265        TCGA-HC-8266        TCGA-HI-7168        TCGA-HI-7169 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HI-7171        TCGA-J4-8198 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
D1V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                43
  CLUS_2               0                46
  CLUS_3               0                25
  CLUS_4               2                58
D1V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               1                29
  CLUS_2               1                68
  CLUS_3               2                75

Clustering(2) Variable = 3p gain mutation analysis
D2V1, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                37
  CLUS_2               1                82
  CLUS_3               1                53
  CLUS_4               0                 1
D2V2, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                51
  CLUS_2               1                49
  CLUS_3               1                67
D2V3, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2               138 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5744        TCGA-CH-5746        TCGA-CH-5748 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752        TCGA-CH-5753 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5754        TCGA-CH-5762        TCGA-CH-5763        TCGA-CH-5764 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772        TCGA-CH-5788 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791        TCGA-CH-5792 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495        TCGA-EJ-5496 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5507        TCGA-EJ-5508 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7321        TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7783        TCGA-EJ-7784 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7791        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FC-7708        TCGA-G9-6332        TCGA-G9-6336        TCGA-G9-6348 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6378        TCGA-G9-6384 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-7510        TCGA-G9-7519 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-7521        TCGA-G9-7522        TCGA-G9-7523        TCGA-G9-7525 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7078        TCGA-HC-7209        TCGA-HC-7210 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HC-7738        TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749        TCGA-HC-7750 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819        TCGA-HC-7820 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HC-7821        TCGA-HC-8256        TCGA-HC-8257        TCGA-HC-8258 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HC-8259        TCGA-HC-8260        TCGA-HC-8261        TCGA-HC-8262 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HC-8265        TCGA-HC-8266        TCGA-HI-7168        TCGA-HI-7169 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HI-7171        TCGA-J4-8198 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D2V4, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2               138 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5744        TCGA-CH-5746        TCGA-CH-5748 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752        TCGA-CH-5753 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5754        TCGA-CH-5762        TCGA-CH-5763        TCGA-CH-5764 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772        TCGA-CH-5788 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791        TCGA-CH-5792 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495        TCGA-EJ-5496 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5507        TCGA-EJ-5508 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7321        TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7783        TCGA-EJ-7784 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7791        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FC-7708        TCGA-G9-6332        TCGA-G9-6336        TCGA-G9-6348 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6378        TCGA-G9-6384 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-7510        TCGA-G9-7519 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-7521        TCGA-G9-7522        TCGA-G9-7523        TCGA-G9-7525 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7078        TCGA-HC-7209        TCGA-HC-7210 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HC-7738        TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749        TCGA-HC-7750 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819        TCGA-HC-7820 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HC-7821        TCGA-HC-8256        TCGA-HC-8257        TCGA-HC-8258 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HC-8259        TCGA-HC-8260        TCGA-HC-8261        TCGA-HC-8262 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HC-8265        TCGA-HC-8266        TCGA-HI-7168        TCGA-HI-7169 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HI-7171        TCGA-J4-8198 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D2V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                44
  CLUS_2               0                46
  CLUS_3               2                23
  CLUS_4               1                59
D2V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                28
  CLUS_2               1                68
  CLUS_3               1                76

Clustering(3) Variable = 3q gain mutation analysis
D3V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                36
  CLUS_2               1                82
  CLUS_3               2                52
  CLUS_4               0                 1
D3V2, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                50
  CLUS_2               1                49
  CLUS_3               2                66
D3V3, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                47
  CLUS_2               0                41
  CLUS_3               0                49
D3V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                38
  CLUS_2               0                43
  CLUS_3               0                56
D3V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2                43
  CLUS_2               0                46
  CLUS_3               2                23
  CLUS_4               2                58
D3V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                27
  CLUS_2               2                67
  CLUS_3               1                76

Clustering(4) Variable = 7p gain mutation analysis
D4V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4                35
  CLUS_2               2                81
  CLUS_3               9                45
  CLUS_4               0                 1
D4V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               7                46
  CLUS_2               1                49
  CLUS_3               7                61
D4V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               7                43
  CLUS_2               1                40
  CLUS_3               6                43
D4V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                36
  CLUS_2               5                38
  CLUS_3               4                52
D4V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                40
  CLUS_2               3                43
  CLUS_3               1                24
  CLUS_4               5                55
D4V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               1                29
  CLUS_2               7                62
  CLUS_3               6                71

Clustering(5) Variable = 7q gain mutation analysis
D5V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                36
  CLUS_2               2                81
  CLUS_3               7                47
  CLUS_4               0                 1
D5V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               6                47
  CLUS_2               1                49
  CLUS_3               5                63
D5V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               5                45
  CLUS_2               1                40
  CLUS_3               5                44
D5V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                38
  CLUS_2               4                39
  CLUS_3               4                52
D5V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                42
  CLUS_2               3                43
  CLUS_3               0                25
  CLUS_4               5                55
D5V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               0                30
  CLUS_2               5                64
  CLUS_3               6                71

Clustering(6) Variable = 8p gain mutation analysis
D6V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                38
  CLUS_2               1                82
  CLUS_3               6                48
  CLUS_4               0                 1
D6V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3                50
  CLUS_2               2                48
  CLUS_3               3                65
D6V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               4                46
  CLUS_2               2                39
  CLUS_3               2                47
D6V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               4                37
  CLUS_2               2                41
  CLUS_3               2                54
D6V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                43
  CLUS_2               2                44
  CLUS_3               1                24
  CLUS_4               3                57
D6V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                29
  CLUS_2               2                67
  CLUS_3               5                72

Clustering(7) Variable = 8q gain mutation analysis
D7V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                37
  CLUS_2               1                82
  CLUS_3              14                40
  CLUS_4               0                 1
D7V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               7                46
  CLUS_2               4                46
  CLUS_3               5                63
D7V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               7                43
  CLUS_2               3                38
  CLUS_3               3                46
D7V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               6                35
  CLUS_2               4                39
  CLUS_3               3                53
D7V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               4                41
  CLUS_2               2                44
  CLUS_3               1                24
  CLUS_4               9                51
D7V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                28
  CLUS_2               3                66
  CLUS_3              11                66

Clustering(8) Variable = 9q gain mutation analysis
D8V1, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                39
  CLUS_2               1                82
  CLUS_3               4                50
  CLUS_4               0                 1
D8V2, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                52
  CLUS_2               0                50
  CLUS_3               3                65
D8V3, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                49
  CLUS_2               0                41
  CLUS_3               3                46
D8V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                40
  CLUS_2               2                41
  CLUS_3               1                55
D8V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                43
  CLUS_2               2                44
  CLUS_3               0                25
  CLUS_4               1                59
D8V6, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                30
  CLUS_2               2                67
  CLUS_3               3                74

Clustering(9) Variable = 12q gain mutation analysis
D9V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 38
  CLUS_2                0                 83
  CLUS_3                2                 52
  CLUS_4                0                  1
D9V2, multiclass
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                169 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5763         TCGA-CH-5764         TCGA-CH-5765 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5766         TCGA-CH-5767         TCGA-CH-5768 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5769         TCGA-CH-5771         TCGA-CH-5772 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5788         TCGA-CH-5789         TCGA-CH-5790 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5791         TCGA-CH-5792         TCGA-CH-5794 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5494         TCGA-EJ-5495         TCGA-EJ-5496 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5497         TCGA-EJ-5498         TCGA-EJ-5499 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5501         TCGA-EJ-5502         TCGA-EJ-5503 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5514         TCGA-EJ-5515         TCGA-EJ-5516 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5517         TCGA-EJ-5518         TCGA-EJ-5519 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5521         TCGA-EJ-5522         TCGA-EJ-5524 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5525         TCGA-EJ-5526         TCGA-EJ-5527 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5530         TCGA-EJ-5531         TCGA-EJ-5532 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5542         TCGA-EJ-7115         TCGA-EJ-7123 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7125         TCGA-EJ-7314         TCGA-EJ-7315 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7317         TCGA-EJ-7321         TCGA-EJ-7327 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7797         TCGA-FC-7708         TCGA-G9-6329 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6499         TCGA-G9-7510         TCGA-G9-7519 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-7522         TCGA-G9-7523         TCGA-G9-7525 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-H9-7775         TCGA-HC-7075         TCGA-HC-7077 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7078         TCGA-HC-7079         TCGA-HC-7080 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7081         TCGA-HC-7209         TCGA-HC-7210 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7211         TCGA-HC-7212         TCGA-HC-7213 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HC-7232 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7233         TCGA-HC-7736         TCGA-HC-7737 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7738         TCGA-HC-7740         TCGA-HC-7742 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7748         TCGA-HC-7749         TCGA-HC-7750 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7752         TCGA-HC-7818         TCGA-HC-7819 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7820         TCGA-HC-7821         TCGA-HC-8256 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-8257         TCGA-HC-8258         TCGA-HC-8259 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-8260         TCGA-HC-8261         TCGA-HC-8262 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-8265         TCGA-HC-8266         TCGA-HI-7168 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-J4-8198 
"12Q GAIN WILD-TYPE" 
D9V3, multiclass
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                138 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5744 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5746         TCGA-CH-5748         TCGA-CH-5750 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5751         TCGA-CH-5752         TCGA-CH-5753 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5754         TCGA-CH-5763         TCGA-CH-5764 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5504 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5505         TCGA-EJ-5507         TCGA-EJ-5508 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-G9-6332         TCGA-G9-6336 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6356         TCGA-G9-6364 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6371 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6378         TCGA-G9-6384 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6494         TCGA-G9-6496         TCGA-G9-7510 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-7519         TCGA-G9-7522         TCGA-G9-7523 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-7525         TCGA-H9-7775         TCGA-HC-7078 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7209         TCGA-HC-7210         TCGA-HC-7211 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7212         TCGA-HC-7213         TCGA-HC-7230 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7231         TCGA-HC-7232         TCGA-HC-7233 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7736         TCGA-HC-7738         TCGA-HC-7742 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7748         TCGA-HC-7749         TCGA-HC-7750 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7752         TCGA-HC-7818         TCGA-HC-7819 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7820         TCGA-HC-7821         TCGA-HC-8256 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-8257         TCGA-HC-8258         TCGA-HC-8259 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-8260         TCGA-HC-8261         TCGA-HC-8262 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-8265         TCGA-HC-8266         TCGA-HI-7168 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7171         TCGA-J4-8198 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
D9V4, multiclass
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                138 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5744 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5746         TCGA-CH-5748         TCGA-CH-5750 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5751         TCGA-CH-5752         TCGA-CH-5753 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5754         TCGA-CH-5763         TCGA-CH-5764 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5504 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5505         TCGA-EJ-5507         TCGA-EJ-5508 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-G9-6332         TCGA-G9-6336 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6356         TCGA-G9-6364 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6371 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6378         TCGA-G9-6384 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6494         TCGA-G9-6496         TCGA-G9-7510 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-7519         TCGA-G9-7522         TCGA-G9-7523 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-7525         TCGA-H9-7775         TCGA-HC-7078 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7209         TCGA-HC-7210         TCGA-HC-7211 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7212         TCGA-HC-7213         TCGA-HC-7230 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7231         TCGA-HC-7232         TCGA-HC-7233 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7736         TCGA-HC-7738         TCGA-HC-7742 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7748         TCGA-HC-7749         TCGA-HC-7750 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7752         TCGA-HC-7818         TCGA-HC-7819 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7820         TCGA-HC-7821         TCGA-HC-8256 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-8257         TCGA-HC-8258         TCGA-HC-8259 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-8260         TCGA-HC-8261         TCGA-HC-8262 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-8265         TCGA-HC-8266         TCGA-HI-7168 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7171         TCGA-J4-8198 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
D9V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                 45
  CLUS_2                1                 45
  CLUS_3                2                 23
  CLUS_4                0                 60
D9V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 28
  CLUS_2                0                 69
  CLUS_3                1                 76

Clustering(10) Variable = 16p gain mutation analysis
D10V1, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                 39
  CLUS_2                1                 82
  CLUS_3                2                 52
  CLUS_4                0                  1
D10V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 52
  CLUS_2                0                 50
  CLUS_3                2                 66
D10V3, multiclass
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                138 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5744 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5746         TCGA-CH-5748         TCGA-CH-5750 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5751         TCGA-CH-5752         TCGA-CH-5753 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5754         TCGA-CH-5762         TCGA-CH-5763 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5764         TCGA-CH-5765         TCGA-CH-5766 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5767         TCGA-CH-5768         TCGA-CH-5769 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5771         TCGA-CH-5772         TCGA-CH-5788 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5789         TCGA-CH-5790         TCGA-CH-5791 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5792         TCGA-CH-5794         TCGA-EJ-5494 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5495         TCGA-EJ-5496         TCGA-EJ-5497 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5498         TCGA-EJ-5499         TCGA-EJ-5501 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5507 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5508         TCGA-EJ-5509         TCGA-EJ-5510 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5511         TCGA-EJ-5512         TCGA-EJ-5514 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5519         TCGA-EJ-5521 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5522         TCGA-EJ-5524         TCGA-EJ-5525 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5526         TCGA-EJ-5527         TCGA-EJ-5530 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7314         TCGA-EJ-7315 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-7317         TCGA-EJ-7321         TCGA-EJ-7327 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-7797         TCGA-FC-7708         TCGA-G9-6332 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6348         TCGA-G9-6356 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G9-6364         TCGA-G9-6365         TCGA-G9-6366 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G9-6371         TCGA-G9-6378         TCGA-G9-6384 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G9-6494         TCGA-G9-6496         TCGA-G9-7510 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G9-7519         TCGA-G9-7521         TCGA-G9-7522 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G9-7523         TCGA-G9-7525         TCGA-H9-7775 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-7078         TCGA-HC-7209         TCGA-HC-7210 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-7211         TCGA-HC-7212         TCGA-HC-7213 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HC-7233 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-7736         TCGA-HC-7738         TCGA-HC-7742 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-7748         TCGA-HC-7749         TCGA-HC-7750 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-7752         TCGA-HC-7818         TCGA-HC-7819 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-7820         TCGA-HC-7821         TCGA-HC-8256 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-8257         TCGA-HC-8258         TCGA-HC-8259 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-8260         TCGA-HC-8261         TCGA-HC-8262 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-8265         TCGA-HC-8266         TCGA-HI-7168 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7171         TCGA-J4-8198 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
D10V4, multiclass
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                138 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5744 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5746         TCGA-CH-5748         TCGA-CH-5750 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5751         TCGA-CH-5752         TCGA-CH-5753 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5754         TCGA-CH-5762         TCGA-CH-5763 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5764         TCGA-CH-5765         TCGA-CH-5766 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5767         TCGA-CH-5768         TCGA-CH-5769 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5771         TCGA-CH-5772         TCGA-CH-5788 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5789         TCGA-CH-5790         TCGA-CH-5791 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CH-5792         TCGA-CH-5794         TCGA-EJ-5494 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5495         TCGA-EJ-5496         TCGA-EJ-5497 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5498         TCGA-EJ-5499         TCGA-EJ-5501 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5507 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5508         TCGA-EJ-5509         TCGA-EJ-5510 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5511         TCGA-EJ-5512         TCGA-EJ-5514 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5519         TCGA-EJ-5521 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5522         TCGA-EJ-5524         TCGA-EJ-5525 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5526         TCGA-EJ-5527         TCGA-EJ-5530 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7314         TCGA-EJ-7315 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-7317         TCGA-EJ-7321         TCGA-EJ-7327 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EJ-7797         TCGA-FC-7708         TCGA-G9-6332 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6348         TCGA-G9-6356 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G9-6364         TCGA-G9-6365         TCGA-G9-6366 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G9-6371         TCGA-G9-6378         TCGA-G9-6384 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G9-6494         TCGA-G9-6496         TCGA-G9-7510 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G9-7519         TCGA-G9-7521         TCGA-G9-7522 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G9-7523         TCGA-G9-7525         TCGA-H9-7775 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-7078         TCGA-HC-7209         TCGA-HC-7210 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-7211         TCGA-HC-7212         TCGA-HC-7213 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HC-7233 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-7736         TCGA-HC-7738         TCGA-HC-7742 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-7748         TCGA-HC-7749         TCGA-HC-7750 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-7752         TCGA-HC-7818         TCGA-HC-7819 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-7820         TCGA-HC-7821         TCGA-HC-8256 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-8257         TCGA-HC-8258         TCGA-HC-8259 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-8260         TCGA-HC-8261         TCGA-HC-8262 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HC-8265         TCGA-HC-8266         TCGA-HI-7168 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7171         TCGA-J4-8198 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
D10V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 43
  CLUS_2                0                 46
  CLUS_3                0                 25
  CLUS_4                1                 59
D10V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                 30
  CLUS_2                2                 67
  CLUS_3                1                 76

Clustering(11) Variable = 16q gain mutation analysis
D11V1, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                 39
  CLUS_2                1                 82
  CLUS_3                2                 52
  CLUS_4                0                  1
D11V2, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 52
  CLUS_2                0                 50
  CLUS_3                2                 66
D11V3, multiclass
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                138 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5744 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5746         TCGA-CH-5748         TCGA-CH-5750 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5751         TCGA-CH-5752         TCGA-CH-5753 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5754         TCGA-CH-5762         TCGA-CH-5763 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5764         TCGA-CH-5765         TCGA-CH-5766 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5767         TCGA-CH-5768         TCGA-CH-5769 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5771         TCGA-CH-5772         TCGA-CH-5788 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5789         TCGA-CH-5790         TCGA-CH-5791 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5792         TCGA-CH-5794         TCGA-EJ-5494 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5495         TCGA-EJ-5496         TCGA-EJ-5497 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5498         TCGA-EJ-5499         TCGA-EJ-5501 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5507 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5508         TCGA-EJ-5509         TCGA-EJ-5510 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5511         TCGA-EJ-5512         TCGA-EJ-5514 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5519         TCGA-EJ-5521 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5522         TCGA-EJ-5524         TCGA-EJ-5525 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5526         TCGA-EJ-5527         TCGA-EJ-5530 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7314         TCGA-EJ-7315 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-7317         TCGA-EJ-7321         TCGA-EJ-7327 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-7797         TCGA-FC-7708         TCGA-G9-6332 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6348         TCGA-G9-6356 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G9-6364         TCGA-G9-6365         TCGA-G9-6366 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G9-6371         TCGA-G9-6378         TCGA-G9-6384 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G9-6494         TCGA-G9-6496         TCGA-G9-7510 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G9-7519         TCGA-G9-7521         TCGA-G9-7522 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G9-7523         TCGA-G9-7525         TCGA-H9-7775 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-7078         TCGA-HC-7209         TCGA-HC-7210 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-7211         TCGA-HC-7212         TCGA-HC-7213 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HC-7233 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-7736         TCGA-HC-7738         TCGA-HC-7742 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-7748         TCGA-HC-7749         TCGA-HC-7750 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-7752         TCGA-HC-7818         TCGA-HC-7819 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-7820         TCGA-HC-7821         TCGA-HC-8256 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-8257         TCGA-HC-8258         TCGA-HC-8259 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-8260         TCGA-HC-8261         TCGA-HC-8262 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-8265         TCGA-HC-8266         TCGA-HI-7168 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7171         TCGA-J4-8198 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
D11V4, multiclass
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                138 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5744 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5746         TCGA-CH-5748         TCGA-CH-5750 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5751         TCGA-CH-5752         TCGA-CH-5753 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5754         TCGA-CH-5762         TCGA-CH-5763 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5764         TCGA-CH-5765         TCGA-CH-5766 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5767         TCGA-CH-5768         TCGA-CH-5769 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5771         TCGA-CH-5772         TCGA-CH-5788 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5789         TCGA-CH-5790         TCGA-CH-5791 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CH-5792         TCGA-CH-5794         TCGA-EJ-5494 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5495         TCGA-EJ-5496         TCGA-EJ-5497 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5498         TCGA-EJ-5499         TCGA-EJ-5501 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5507 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5508         TCGA-EJ-5509         TCGA-EJ-5510 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5511         TCGA-EJ-5512         TCGA-EJ-5514 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5519         TCGA-EJ-5521 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5522         TCGA-EJ-5524         TCGA-EJ-5525 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5526         TCGA-EJ-5527         TCGA-EJ-5530 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7314         TCGA-EJ-7315 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-7317         TCGA-EJ-7321         TCGA-EJ-7327 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EJ-7797         TCGA-FC-7708         TCGA-G9-6332 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6348         TCGA-G9-6356 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G9-6364         TCGA-G9-6365         TCGA-G9-6366 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G9-6371         TCGA-G9-6378         TCGA-G9-6384 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G9-6494         TCGA-G9-6496         TCGA-G9-7510 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G9-7519         TCGA-G9-7521         TCGA-G9-7522 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G9-7523         TCGA-G9-7525         TCGA-H9-7775 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-7078         TCGA-HC-7209         TCGA-HC-7210 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-7211         TCGA-HC-7212         TCGA-HC-7213 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HC-7233 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-7736         TCGA-HC-7738         TCGA-HC-7742 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-7748         TCGA-HC-7749         TCGA-HC-7750 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-7752         TCGA-HC-7818         TCGA-HC-7819 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-7820         TCGA-HC-7821         TCGA-HC-8256 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-8257         TCGA-HC-8258         TCGA-HC-8259 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-8260         TCGA-HC-8261         TCGA-HC-8262 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HC-8265         TCGA-HC-8266         TCGA-HI-7168 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7171         TCGA-J4-8198 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
D11V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 43
  CLUS_2                0                 46
  CLUS_3                0                 25
  CLUS_4                1                 59
D11V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                 30
  CLUS_2                2                 67
  CLUS_3                1                 76

Clustering(12) Variable = 5q loss mutation analysis
D12V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                39
  CLUS_2               0                83
  CLUS_3               3                51
  CLUS_4               0                 1
D12V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3                50
  CLUS_2               0                50
  CLUS_3               0                68
D12V3, multiclass
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2               138 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5744        TCGA-CH-5746        TCGA-CH-5748 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752        TCGA-CH-5753 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CH-5754        TCGA-CH-5762        TCGA-CH-5763        TCGA-CH-5764 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772        TCGA-CH-5788 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791        TCGA-CH-5792 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495        TCGA-EJ-5496 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5507        TCGA-EJ-5508 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-7321        TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-7791        TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-7797        TCGA-FC-7708        TCGA-G9-6332        TCGA-G9-6336 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G9-6348        TCGA-G9-6356        TCGA-G9-6364        TCGA-G9-6365 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G9-6366        TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6378 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G9-6384        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-7510 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G9-7519        TCGA-G9-7521        TCGA-G9-7522        TCGA-G9-7523 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G9-7525        TCGA-H9-7775        TCGA-HC-7078        TCGA-HC-7209 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HC-7230        TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7233 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HC-7736        TCGA-HC-7738        TCGA-HC-7742        TCGA-HC-7744 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HC-7820        TCGA-HC-7821        TCGA-HC-8256        TCGA-HC-8257 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HC-8258        TCGA-HC-8259        TCGA-HC-8260        TCGA-HC-8261 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HC-8262        TCGA-HC-8265        TCGA-HC-8266        TCGA-HI-7169 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HI-7171        TCGA-J4-8198 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
D12V4, multiclass
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2               138 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5744        TCGA-CH-5746        TCGA-CH-5748 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752        TCGA-CH-5753 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CH-5754        TCGA-CH-5762        TCGA-CH-5763        TCGA-CH-5764 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772        TCGA-CH-5788 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791        TCGA-CH-5792 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495        TCGA-EJ-5496 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5507        TCGA-EJ-5508 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-7321        TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-7791        TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EJ-7797        TCGA-FC-7708        TCGA-G9-6332        TCGA-G9-6336 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G9-6348        TCGA-G9-6356        TCGA-G9-6364        TCGA-G9-6365 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G9-6366        TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6378 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G9-6384        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-7510 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G9-7519        TCGA-G9-7521        TCGA-G9-7522        TCGA-G9-7523 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G9-7525        TCGA-H9-7775        TCGA-HC-7078        TCGA-HC-7209 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HC-7230        TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7233 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HC-7736        TCGA-HC-7738        TCGA-HC-7742        TCGA-HC-7744 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HC-7820        TCGA-HC-7821        TCGA-HC-8256        TCGA-HC-8257 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HC-8258        TCGA-HC-8259        TCGA-HC-8260        TCGA-HC-8261 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HC-8262        TCGA-HC-8265        TCGA-HC-8266        TCGA-HI-7169 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HI-7171        TCGA-J4-8198 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
D12V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               2                43
  CLUS_2               0                46
  CLUS_3               1                24
  CLUS_4               0                60
D12V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2               1                68
  CLUS_3               2                75

Clustering(13) Variable = 6q loss mutation analysis
D13V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                37
  CLUS_2               0                83
  CLUS_3               5                49
  CLUS_4               0                 1
D13V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               4                49
  CLUS_2               0                50
  CLUS_3               3                65
D13V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               5                45
  CLUS_2               0                41
  CLUS_3               2                47
D13V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               5                36
  CLUS_2               2                41
  CLUS_3               0                56
D13V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3                42
  CLUS_2               0                46
  CLUS_3               1                24
  CLUS_4               3                57
D13V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3                27
  CLUS_2               1                68
  CLUS_3               3                74

Clustering(14) Variable = 8p loss mutation analysis
D14V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               7                32
  CLUS_2              13                70
  CLUS_3              26                28
  CLUS_4               0                 1
D14V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              11                42
  CLUS_2               4                46
  CLUS_3              27                41
D14V3, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              11                39
  CLUS_2               6                35
  CLUS_3              20                29
D14V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              10                31
  CLUS_2              19                24
  CLUS_3               8                48
D14V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              22                23
  CLUS_2               4                42
  CLUS_3               6                19
  CLUS_4              13                47
D14V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               6                24
  CLUS_2              17                52
  CLUS_3              22                55

Clustering(15) Variable = 8q loss mutation analysis
D15V1, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                39
  CLUS_2               0                83
  CLUS_3               4                50
  CLUS_4               0                 1
D15V2, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                52
  CLUS_2               0                50
  CLUS_3               3                65
D15V3, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                49
  CLUS_2               0                41
  CLUS_3               3                46
D15V4, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                40
  CLUS_2               3                40
  CLUS_3               0                56
D15V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3                42
  CLUS_2               0                46
  CLUS_3               1                24
  CLUS_4               0                60
D15V6, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2               3                66
  CLUS_3               1                76

Clustering(16) Variable = 10p loss mutation analysis
D16V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                 39
  CLUS_2                2                 81
  CLUS_3                4                 50
  CLUS_4                0                  1
D16V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                 51
  CLUS_2                0                 50
  CLUS_3                4                 64
D16V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                3                 47
  CLUS_2                0                 41
  CLUS_3                2                 47
D16V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                3                 38
  CLUS_2                1                 42
  CLUS_3                1                 55
D16V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                 43
  CLUS_2                0                 46
  CLUS_3                2                 23
  CLUS_4                2                 58
D16V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                3                 27
  CLUS_2                1                 68
  CLUS_3                2                 75

Clustering(17) Variable = 10q loss mutation analysis
D17V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                 39
  CLUS_2                2                 81
  CLUS_3                3                 51
  CLUS_4                0                  1
D17V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                 52
  CLUS_2                1                 49
  CLUS_3                3                 65
D17V3, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                 49
  CLUS_2                1                 40
  CLUS_3                3                 46
D17V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                 40
  CLUS_2                2                 41
  CLUS_3                2                 54
D17V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                2                 43
  CLUS_2                0                 46
  CLUS_3                1                 24
  CLUS_4                2                 58
D17V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                 29
  CLUS_2                2                 67
  CLUS_3                2                 75

Clustering(18) Variable = 12p loss mutation analysis
D18V1, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 39
  CLUS_2                4                 79
  CLUS_3                5                 49
  CLUS_4                0                  1
D18V2, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                2                 51
  CLUS_2                0                 50
  CLUS_3                6                 62
D18V3, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                2                 48
  CLUS_2                2                 39
  CLUS_3                4                 45
D18V4, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                2                 39
  CLUS_2                3                 40
  CLUS_3                3                 53
D18V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                4                 41
  CLUS_2                4                 42
  CLUS_3                1                 24
  CLUS_4                0                 60
D18V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 29
  CLUS_2                6                 63
  CLUS_3                2                 75

Clustering(19) Variable = 13q loss mutation analysis
D19V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                 37
  CLUS_2                1                 82
  CLUS_3                9                 45
  CLUS_4                0                  1
D19V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                3                 50
  CLUS_2                1                 49
  CLUS_3                7                 61
D19V3, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                4                 46
  CLUS_2                0                 41
  CLUS_3                7                 42
D19V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                4                 37
  CLUS_2                5                 38
  CLUS_3                2                 54
D19V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                5                 40
  CLUS_2                4                 42
  CLUS_3                2                 23
  CLUS_4                1                 59
D19V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                 28
  CLUS_2                7                 62
  CLUS_3                3                 74

Clustering(20) Variable = 16q loss mutation analysis
D20V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 37
  CLUS_2                3                 80
  CLUS_3               17                 37
  CLUS_4                0                  1
D20V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                8                 45
  CLUS_2                2                 48
  CLUS_3               10                 58
D20V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                8                 42
  CLUS_2                2                 39
  CLUS_3                8                 41
D20V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                7                 34
  CLUS_2                8                 35
  CLUS_3                3                 53
D20V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                8                 37
  CLUS_2                2                 44
  CLUS_3                2                 23
  CLUS_4                9                 51
D20V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 28
  CLUS_2                8                 61
  CLUS_3               11                 66

Clustering(21) Variable = 17p loss mutation analysis
D21V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                 39
  CLUS_2                3                 80
  CLUS_3               15                 39
  CLUS_4                0                  1
D21V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                8                 45
  CLUS_2                2                 48
  CLUS_3                8                 60
D21V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                7                 43
  CLUS_2                2                 39
  CLUS_3                7                 42
D21V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                7                 34
  CLUS_2                7                 36
  CLUS_3                2                 54
D21V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                7                 38
  CLUS_2                3                 43
  CLUS_3                3                 22
  CLUS_4                5                 55
D21V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                 27
  CLUS_2                9                 60
  CLUS_3                6                 71

Clustering(22) Variable = 18p loss mutation analysis
D22V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                 38
  CLUS_2                2                 81
  CLUS_3               16                 38
  CLUS_4                0                  1
D22V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                9                 44
  CLUS_2                3                 47
  CLUS_3                6                 62
D22V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                7                 43
  CLUS_2                3                 38
  CLUS_3                5                 44
D22V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                5                 36
  CLUS_2                7                 36
  CLUS_3                3                 53
D22V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                4                 41
  CLUS_2                1                 45
  CLUS_3                2                 23
  CLUS_4               11                 49
D22V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                 29
  CLUS_2                3                 66
  CLUS_3               14                 63

Clustering(23) Variable = 18q loss mutation analysis
D23V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                 39
  CLUS_2                3                 80
  CLUS_3               21                 33
  CLUS_4                0                  1
D23V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                8                 45
  CLUS_2                4                 46
  CLUS_3               11                 57
D23V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                7                 43
  CLUS_2                3                 38
  CLUS_3                9                 40
D23V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                5                 36
  CLUS_2               10                 33
  CLUS_3                4                 52
D23V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                9                 36
  CLUS_2                2                 44
  CLUS_3                2                 23
  CLUS_4               10                 50
D23V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 29
  CLUS_2                7                 62
  CLUS_3               15                 62

Clustering(24) Variable = 20p loss mutation analysis
D24V1, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                 38
  CLUS_2                1                 82
  CLUS_3                2                 52
  CLUS_4                0                  1
D24V2, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                3                 50
  CLUS_2                0                 50
  CLUS_3                1                 67
D24V3, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                3                 47
  CLUS_2                0                 41
  CLUS_3                1                 48
D24V4, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                3                 38
  CLUS_2                0                 43
  CLUS_3                1                 55
D24V5, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                0                 45
  CLUS_2                1                 45
  CLUS_3                3                 22
  CLUS_4                0                 60
D24V6, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                3                 27
  CLUS_2                0                 69
  CLUS_3                1                 76

Clustering(25) Variable = 21q loss mutation analysis
D25V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                 39
  CLUS_2                1                 82
  CLUS_3                3                 51
  CLUS_4                0                  1
D25V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 51
  CLUS_2                0                 50
  CLUS_3                1                 67
D25V3, multiclass
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                138 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5744 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5746         TCGA-CH-5748         TCGA-CH-5750 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5751         TCGA-CH-5752         TCGA-CH-5753 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5754         TCGA-CH-5762         TCGA-CH-5763 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5764         TCGA-CH-5765         TCGA-CH-5766 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5767         TCGA-CH-5768         TCGA-CH-5769 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5771         TCGA-CH-5772         TCGA-CH-5788 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5789         TCGA-CH-5790         TCGA-CH-5791 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5792         TCGA-CH-5794         TCGA-EJ-5494 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5495         TCGA-EJ-5496         TCGA-EJ-5497 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5498         TCGA-EJ-5499         TCGA-EJ-5501 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5507 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5508         TCGA-EJ-5509         TCGA-EJ-5510 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5511         TCGA-EJ-5512         TCGA-EJ-5514 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5521         TCGA-EJ-5522 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FC-7708         TCGA-G9-6332         TCGA-G9-6336 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6356         TCGA-G9-6364 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6371 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6378         TCGA-G9-6384 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G9-6494         TCGA-G9-6496         TCGA-G9-7510 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G9-7519         TCGA-G9-7521         TCGA-G9-7522 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G9-7523         TCGA-G9-7525         TCGA-H9-7775 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-7078         TCGA-HC-7209         TCGA-HC-7210 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-7211         TCGA-HC-7212         TCGA-HC-7213 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HC-7232 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-7233         TCGA-HC-7736         TCGA-HC-7738 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7749         TCGA-HC-7750 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-7752         TCGA-HC-7818         TCGA-HC-7819 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-7820         TCGA-HC-7821         TCGA-HC-8256 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-8257         TCGA-HC-8258         TCGA-HC-8259 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-8260         TCGA-HC-8261         TCGA-HC-8262 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-8265         TCGA-HC-8266         TCGA-HI-7168 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7171         TCGA-J4-8198 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
D25V4, multiclass
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                138 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5744 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5746         TCGA-CH-5748         TCGA-CH-5750 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5751         TCGA-CH-5752         TCGA-CH-5753 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5754         TCGA-CH-5762         TCGA-CH-5763 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5764         TCGA-CH-5765         TCGA-CH-5766 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5767         TCGA-CH-5768         TCGA-CH-5769 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5771         TCGA-CH-5772         TCGA-CH-5788 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5789         TCGA-CH-5790         TCGA-CH-5791 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CH-5792         TCGA-CH-5794         TCGA-EJ-5494 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5495         TCGA-EJ-5496         TCGA-EJ-5497 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5498         TCGA-EJ-5499         TCGA-EJ-5501 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5507 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5508         TCGA-EJ-5509         TCGA-EJ-5510 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5511         TCGA-EJ-5512         TCGA-EJ-5514 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5521         TCGA-EJ-5522 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FC-7708         TCGA-G9-6332         TCGA-G9-6336 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6356         TCGA-G9-6364 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6371 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6378         TCGA-G9-6384 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G9-6494         TCGA-G9-6496         TCGA-G9-7510 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G9-7519         TCGA-G9-7521         TCGA-G9-7522 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G9-7523         TCGA-G9-7525         TCGA-H9-7775 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-7078         TCGA-HC-7209         TCGA-HC-7210 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-7211         TCGA-HC-7212         TCGA-HC-7213 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HC-7232 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-7233         TCGA-HC-7736         TCGA-HC-7738 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7749         TCGA-HC-7750 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-7752         TCGA-HC-7818         TCGA-HC-7819 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-7820         TCGA-HC-7821         TCGA-HC-8256 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-8257         TCGA-HC-8258         TCGA-HC-8259 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-8260         TCGA-HC-8261         TCGA-HC-8262 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HC-8265         TCGA-HC-8266         TCGA-HI-7168 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7171         TCGA-J4-8198 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
D25V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 43
  CLUS_2                2                 44
  CLUS_3                0                 25
  CLUS_4                0                 60
D25V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2                2                 67
  CLUS_3                2                 75

Clustering(26) Variable = 22q loss mutation analysis
D26V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                 38
  CLUS_2                0                 83
  CLUS_3                5                 49
  CLUS_4                0                  1
D26V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                 51
  CLUS_2                0                 50
  CLUS_3                3                 65
D26V3, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                 48
  CLUS_2                0                 41
  CLUS_3                3                 46
D26V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                 39
  CLUS_2                3                 40
  CLUS_3                0                 56
D26V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                 43
  CLUS_2                1                 45
  CLUS_3                2                 23
  CLUS_4                1                 59
D26V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                 29
  CLUS_2                2                 67
  CLUS_3                3                 74
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"          "MRNASEQ_CNMF" 
                     V4                      V5                      V6 
"MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
