
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/335574/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/READ-TP/2667054/1.GDAC_mergedClustering.Finished/READ-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=READ-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=READ-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=166, in cluster file=162, common to both=162
[1] "Reduce the number of clustering variables from 80 to 75."
[1]  75 162
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4               158 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4               158 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               27               135 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               27               135 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               20               142 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               20               142 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               21               141 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               21               141 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               17               145 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               17               145 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               23               139 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               23               139 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               158 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               158 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               159 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               159 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               20               142 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               20               142 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12               150 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12               150 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               27               135 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               27               135 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               27               135 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               27               135 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               90                72 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               90                72 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               79                83 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               79                83 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               27               135 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               27               135 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               72                90 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               72                90 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               35               127 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               35               127 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               26               136 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               26               136 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                154 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                154 
[1] "10q gain mutation analysis"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                158 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                158 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                21                141 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                21                141 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                17                145 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                17                145 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                28                134 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                28                134 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                19                143 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                19                143 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               102                 60 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               102                 60 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                158 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                158 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                29                133 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                29                133 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                30                132 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                30                132 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                159 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                159 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                144 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                144 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                155 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                155 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                158 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                158 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                20                142 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                20                142 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                23                139 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                23                139 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                95                 67 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                95                 67 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               132                 30 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               132                 30 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                155 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                155 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                157 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                157 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7               155 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7               155 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               21               141 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               21               141 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                7               155 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                7               155 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5               157 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5               157 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                8               154 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                8               154 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               158 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               158 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               39               123 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               39               123 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               46               116 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               46               116 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11               151 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11               151 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               23               139 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               23               139 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8               154 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8               154 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               14               148 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               14               148 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               56               106 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               56               106 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               159 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               159 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               12               150 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               12               150 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11               151 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11               151 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                17                145 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                17                145 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                21                141 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                21                141 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                19                143 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                19                143 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                23                139 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                23                139 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                12                150 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                12                150 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                154 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                154 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                157 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                157 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                51                111 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                51                111 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                58                104 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                58                104 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                156 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                156 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                152 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                152 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                89                 73 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                89                 73 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                15                147 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                15                147 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               114                 48 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               114                 48 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               126                 36 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               126                 36 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 7                155 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 7                155 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 7                155 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 7                155 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                144 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                144 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                43                119 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                43                119 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                42                120 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                42                120 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6               156 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6               156 
[1] "data2feature, selection=ALL"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
 [4] "METHLYATION_CNMF"      "RPPA_CNMF"             "RPPA_CHIERARCHICAL"   
 [7] "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"          
[10] "MIRSEQ_CHIERARCHICAL" 

Input Data has 10 rows and 162 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
 [4] "METHLYATION_CNMF"      "RPPA_CNMF"             "RPPA_CHIERARCHICAL"   
 [7] "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"          
[10] "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 162 columns, 0 survival variables, and 10 non-survival variables.
MRNA_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=5, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                68 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3593        TCGA-AG-3594 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600        TCGA-AG-3601 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608        TCGA-AG-3609 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726        TCGA-AG-3727 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3728        TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3902        TCGA-AG-3909 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4005        TCGA-AG-4007 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A002        TCGA-AG-A008 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A023        TCGA-AG-A025 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02X        TCGA-AG-A032 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V2, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                68 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3593        TCGA-AG-3594 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600        TCGA-AG-3601 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608        TCGA-AG-3609 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726        TCGA-AG-3727 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3728        TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3902        TCGA-AG-3909 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4005        TCGA-AG-4007 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A002        TCGA-AG-A008 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A023        TCGA-AG-A025 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02X        TCGA-AG-A032 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V3, multiclass
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                26
  CLUS_2               1                37
  CLUS_3               2                27
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                52
  CLUS_2               1                32
  CLUS_3               1                39
D1V6, multiclass
D1V7, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                70 
       TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400        TCGA-AF-3913 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578        TCGA-AG-3580 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3584 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3586        TCGA-AG-3593        TCGA-AG-3594        TCGA-AG-3598 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3600        TCGA-AG-3601        TCGA-AG-3602 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3605        TCGA-AG-3608        TCGA-AG-3609        TCGA-AG-3611 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3612        TCGA-AG-3726        TCGA-AG-3727        TCGA-AG-3728 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882        TCGA-AG-3883 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890        TCGA-AG-3892 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3901        TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L        TCGA-AG-A01N 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A023 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02N 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A02X        TCGA-AG-A032 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V8, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                70 
       TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400        TCGA-AF-3913 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578        TCGA-AG-3580 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3584 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3586        TCGA-AG-3593        TCGA-AG-3594        TCGA-AG-3598 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3600        TCGA-AG-3601        TCGA-AG-3602 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3605        TCGA-AG-3608        TCGA-AG-3609        TCGA-AG-3611 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3612        TCGA-AG-3726        TCGA-AG-3727        TCGA-AG-3728 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882        TCGA-AG-3883 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890        TCGA-AG-3892 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3901        TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L        TCGA-AG-A01N 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A023 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02N 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A02X        TCGA-AG-A032 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V9, multiclass
D1V10, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                19
  CLUS_2               1                62
  CLUS_3               2                57

Clustering(2) Variable = 1q gain mutation analysis
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3                22
  CLUS_2               4                16
  CLUS_3               5                19
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               4                15
  CLUS_2               4                20
  CLUS_3               4                22
D2V3, multiclass
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                24
  CLUS_2               6                32
  CLUS_3               8                21
D2V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              13                40
  CLUS_2               2                31
  CLUS_3               6                34
D2V6, multiclass
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               1                16
  CLUS_3               5                11
  CLUS_4               4                16
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                15
  CLUS_2               5                19
  CLUS_3               6                24
D2V9, multiclass
D2V10, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                17
  CLUS_2              11                52
  CLUS_3               8                51

Clustering(3) Variable = 2p gain mutation analysis
D3V1, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                23
  CLUS_2               0                20
  CLUS_3               4                20
D3V2, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               3                16
  CLUS_2               2                22
  CLUS_3               1                25
D3V3, multiclass
D3V4, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               5                21
  CLUS_2               5                33
  CLUS_3               3                26
D3V5, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               7                46
  CLUS_2               6                27
  CLUS_3               4                36
D3V6, multiclass
D3V7, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               1                16
  CLUS_3               4                12
  CLUS_4               0                20
D3V8, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                16
  CLUS_2               0                24
  CLUS_3               5                25
D3V9, multiclass
D3V10, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2               6                57
  CLUS_3              10                49

Clustering(4) Variable = 2q gain mutation analysis
D4V1, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                23
  CLUS_2               0                20
  CLUS_3               6                18
D4V2, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               5                14
  CLUS_2               2                22
  CLUS_3               1                25
D4V3, multiclass
D4V4, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               4                22
  CLUS_2               4                34
  CLUS_3               4                25
D4V5, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               6                47
  CLUS_2               6                27
  CLUS_3               5                35
D4V6, multiclass
D4V7, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               3                14
  CLUS_3               4                12
  CLUS_4               0                20
D4V8, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                16
  CLUS_2               0                24
  CLUS_3               7                23
D4V9, multiclass
D4V10, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2               8                55
  CLUS_3               8                51

Clustering(5) Variable = 3p gain mutation analysis
D5V1, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                24
  CLUS_2               1                19
  CLUS_3               2                22
D5V2, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                17
  CLUS_2               1                23
  CLUS_3               1                25
D5V3, multiclass
D5V4, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               5                21
  CLUS_2               4                34
  CLUS_3               4                25
D5V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               9                44
  CLUS_2               3                30
  CLUS_3               1                39
D5V6, multiclass
D5V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               1                16
  CLUS_3               1                15
  CLUS_4               1                19
D5V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                16
  CLUS_2               2                22
  CLUS_3               1                29
D5V9, multiclass
D5V10, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                19
  CLUS_2               4                59
  CLUS_3              12                47

Clustering(6) Variable = 3q gain mutation analysis
D6V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                22
  CLUS_2               2                18
  CLUS_3               3                21
D6V2, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                16
  CLUS_2               2                22
  CLUS_3               3                23
D6V3, multiclass
D6V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               4                22
  CLUS_2               6                32
  CLUS_3               5                24
D6V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              11                42
  CLUS_2               5                28
  CLUS_3               1                39
D6V6, multiclass
D6V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               3                14
  CLUS_3               2                14
  CLUS_4               1                19
D6V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                16
  CLUS_2               2                22
  CLUS_3               5                25
D6V9, multiclass
D6V10, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                19
  CLUS_2               8                55
  CLUS_3              13                46

Clustering(7) Variable = 4p gain mutation analysis
D7V1, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                68 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3728        TCGA-AG-3878        TCGA-AG-3881 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3890        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3902 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4005 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A002 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A023        TCGA-AG-A025 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02X        TCGA-AG-A032 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V2, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                68 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3728        TCGA-AG-3878        TCGA-AG-3881 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3890        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3902 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4005 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A002 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A023        TCGA-AG-A025 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02X        TCGA-AG-A032 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V3, multiclass
D7V4, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                25
  CLUS_2               1                37
  CLUS_3               1                28
D7V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                51
  CLUS_2               0                33
  CLUS_3               2                38
D7V6, multiclass
D7V7, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                70 
       TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400        TCGA-AF-3913 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578        TCGA-AG-3580 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3584 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593        TCGA-AG-3594 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600        TCGA-AG-3601 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608        TCGA-AG-3609 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726        TCGA-AG-3727 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3728        TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3909        TCGA-AG-3999 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-4001        TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-4015        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A014        TCGA-AG-A015 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L        TCGA-AG-A01N 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A023 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02N 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A02X        TCGA-AG-A032 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V8, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                70 
       TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400        TCGA-AF-3913 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578        TCGA-AG-3580 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3584 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593        TCGA-AG-3594 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600        TCGA-AG-3601 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608        TCGA-AG-3609 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726        TCGA-AG-3727 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3728        TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3909        TCGA-AG-3999 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-4001        TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-4015        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A014        TCGA-AG-A015 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L        TCGA-AG-A01N 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A023 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02N 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A02X        TCGA-AG-A032 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V9, multiclass
D7V10, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                19
  CLUS_2               1                62
  CLUS_3               3                56

Clustering(8) Variable = 4q gain mutation analysis
D8V1, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                67 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3728        TCGA-AG-3878        TCGA-AG-3881 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3890        TCGA-AG-3892        TCGA-AG-3894        TCGA-AG-3896 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3909        TCGA-AG-3999 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-4001        TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-4015        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02X        TCGA-AG-A032 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V2, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                67 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3728        TCGA-AG-3878        TCGA-AG-3881 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3890        TCGA-AG-3892        TCGA-AG-3894        TCGA-AG-3896 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3909        TCGA-AG-3999 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-4001        TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-4015        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02X        TCGA-AG-A032 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V3, multiclass
D8V4, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                92 
       TCGA-AF-2687        TCGA-AF-2690        TCGA-AF-2693        TCGA-AF-3911 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-4110        TCGA-AF-6136        TCGA-AF-6655        TCGA-AF-6672 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3591        TCGA-AG-3592        TCGA-AG-3725        TCGA-AG-3731 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3732        TCGA-AG-3742        TCGA-AG-4021        TCGA-AG-4022 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A026 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6644        TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621        TCGA-CI-6622 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957        TCGA-CL-5917 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749        TCGA-DC-5337 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155        TCGA-DC-6156 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE        TCGA-DY-A1DF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DY-A1H8        TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6511        TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6881        TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6885        TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863        TCGA-F5-6864 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572        TCGA-G5-6641 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1                52
  CLUS_2               0                33
  CLUS_3               2                38
D8V6, multiclass
D8V7, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                70 
       TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400        TCGA-AF-3913 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578        TCGA-AG-3580 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3584 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593        TCGA-AG-3594 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600        TCGA-AG-3601 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608        TCGA-AG-3609 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726        TCGA-AG-3727 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3728        TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3892        TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3901        TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L        TCGA-AG-A01N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A023 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A02X        TCGA-AG-A032 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V8, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                70 
       TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400        TCGA-AF-3913 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578        TCGA-AG-3580 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3584 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593        TCGA-AG-3594 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600        TCGA-AG-3601 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608        TCGA-AG-3609 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726        TCGA-AG-3727 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3728        TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3892        TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3901        TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L        TCGA-AG-A01N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A023 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A02X        TCGA-AG-A032 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V9, multiclass
D8V10, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2               1                62
  CLUS_3               1                58

Clustering(9) Variable = 5p gain mutation analysis
D9V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4                21
  CLUS_2               2                18
  CLUS_3               4                20
D9V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                16
  CLUS_2               3                21
  CLUS_3               4                22
D9V3, multiclass
D9V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4                22
  CLUS_2               1                37
  CLUS_3               5                24
D9V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               8                45
  CLUS_2               5                28
  CLUS_3               4                36
D9V6, multiclass
D9V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               2                15
  CLUS_3               4                12
  CLUS_4               2                18
D9V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                16
  CLUS_2               2                22
  CLUS_3               7                23
D9V9, multiclass
D9V10, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2               9                54
  CLUS_3               7                52

Clustering(10) Variable = 5q gain mutation analysis
D10V1, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                23
  CLUS_2               1                19
  CLUS_3               4                20
D10V2, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                16
  CLUS_2               1                23
  CLUS_3               3                23
D10V3, multiclass
D10V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                25
  CLUS_2               0                38
  CLUS_3               4                25
D10V5, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                50
  CLUS_2               3                30
  CLUS_3               3                37
D10V6, multiclass
D10V7, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               2                15
  CLUS_3               2                14
  CLUS_4               1                19
D10V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                16
  CLUS_2               1                23
  CLUS_3               5                25
D10V9, multiclass
D10V10, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                19
  CLUS_2               6                57
  CLUS_3               3                56

Clustering(11) Variable = 6p gain mutation analysis
D11V1, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                23
  CLUS_2               3                17
  CLUS_3               5                19
D11V2, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               5                14
  CLUS_2               2                22
  CLUS_3               3                23
D11V3, multiclass
D11V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               9                17
  CLUS_2               2                36
  CLUS_3               6                23
D11V5, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              11                42
  CLUS_2               4                29
  CLUS_3               5                35
D11V6, multiclass
D11V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               5                12
  CLUS_3               2                14
  CLUS_4               1                19
D11V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               0                17
  CLUS_2               2                22
  CLUS_3               8                22
D11V9, multiclass
D11V10, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               3                16
  CLUS_2              10                53
  CLUS_3              13                46

Clustering(12) Variable = 6q gain mutation analysis
D12V1, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               2                23
  CLUS_2               3                17
  CLUS_3               5                19
D12V2, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               5                14
  CLUS_2               2                22
  CLUS_3               3                23
D12V3, multiclass
D12V4, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               8                18
  CLUS_2               3                35
  CLUS_3               6                23
D12V5, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1              11                42
  CLUS_2               4                29
  CLUS_3               5                35
D12V6, multiclass
D12V7, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               5                12
  CLUS_3               2                14
  CLUS_4               1                19
D12V8, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                17
  CLUS_2               2                22
  CLUS_3               8                22
D12V9, multiclass
D12V10, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               3                16
  CLUS_2              10                53
  CLUS_3              13                46

Clustering(13) Variable = 7p gain mutation analysis
D13V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                20
  CLUS_2              11                 9
  CLUS_3              16                 8
D13V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              14                 5
  CLUS_2               5                19
  CLUS_3              13                13
D13V3, multiclass
D13V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              20                 6
  CLUS_2              17                21
  CLUS_3              21                 8
D13V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              34                19
  CLUS_2              18                15
  CLUS_3              22                18
D13V6, multiclass
D13V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              11                 7
  CLUS_2               7                10
  CLUS_3              10                 6
  CLUS_4               4                16
D13V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               8                 9
  CLUS_2               5                19
  CLUS_3              19                11
D13V9, multiclass
D13V10, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              13                 6
  CLUS_2              27                36
  CLUS_3              38                21

Clustering(14) Variable = 7q gain mutation analysis
D14V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               5                20
  CLUS_2              11                 9
  CLUS_3              15                 9
D14V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              13                 6
  CLUS_2               5                19
  CLUS_3              13                13
D14V3, multiclass
D14V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              16                10
  CLUS_2              14                24
  CLUS_3              17                12
D14V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              28                25
  CLUS_2              16                17
  CLUS_3              20                20
D14V6, multiclass
D14V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              11                 7
  CLUS_2               8                 9
  CLUS_3               8                 8
  CLUS_4               4                16
D14V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               8                 9
  CLUS_2               5                19
  CLUS_3              18                12
D14V9, multiclass
D14V10, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              11                 8
  CLUS_2              27                36
  CLUS_3              32                27

Clustering(15) Variable = 8p gain mutation analysis
D15V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3                22
  CLUS_2               2                18
  CLUS_3               5                19
D15V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               5                14
  CLUS_2               3                21
  CLUS_3               2                24
D15V3, multiclass
D15V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               4                22
  CLUS_2               6                32
  CLUS_3               7                22
D15V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               5                48
  CLUS_2               7                26
  CLUS_3              11                29
D15V6, multiclass
D15V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               3                14
  CLUS_3               3                13
  CLUS_4               3                17
D15V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                16
  CLUS_2               4                20
  CLUS_3               6                24
D15V9, multiclass
D15V10, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               5                14
  CLUS_2               9                54
  CLUS_3              10                49

Clustering(16) Variable = 8q gain mutation analysis
D16V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               7                18
  CLUS_2               8                12
  CLUS_3              17                 7
D16V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              14                 5
  CLUS_2               8                16
  CLUS_3              10                16
D16V3, multiclass
D16V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              14                12
  CLUS_2              15                23
  CLUS_3              12                17
D16V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              19                34
  CLUS_2              17                16
  CLUS_3              23                17
D16V6, multiclass
D16V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               7                11
  CLUS_2              11                 6
  CLUS_3               9                 7
  CLUS_4               5                15
D16V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               9                 8
  CLUS_2               6                18
  CLUS_3              17                13
D16V9, multiclass
D16V10, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              12                 7
  CLUS_2              28                35
  CLUS_3              25                34

Clustering(17) Variable = 9p gain mutation analysis
D17V1, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                23
  CLUS_2               8                12
  CLUS_3               6                18
D17V2, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4                15
  CLUS_2               3                21
  CLUS_3               9                17
D17V3, multiclass
D17V4, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                24
  CLUS_2               7                31
  CLUS_3              10                19
D17V5, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1              14                39
  CLUS_2               8                25
  CLUS_3               7                33
D17V6, multiclass
D17V7, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               4                13
  CLUS_3               3                13
  CLUS_4               5                15
D17V8, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3                14
  CLUS_2               7                17
  CLUS_3               6                24
D17V9, multiclass
D17V10, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3                16
  CLUS_2              15                48
  CLUS_3              11                48

Clustering(18) Variable = 9q gain mutation analysis
D18V1, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                24
  CLUS_2               6                14
  CLUS_3               5                19
D18V2, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3                16
  CLUS_2               2                22
  CLUS_3               7                19
D18V3, multiclass
D18V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                24
  CLUS_2               6                32
  CLUS_3               6                23
D18V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1              12                41
  CLUS_2               6                27
  CLUS_3               5                35
D18V6, multiclass
D18V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               2                15
  CLUS_3               0                16
  CLUS_4               5                15
D18V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3                14
  CLUS_2               7                17
  CLUS_3               1                29
D18V9, multiclass
D18V10, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2              11                52
  CLUS_3               9                50

Clustering(19) Variable = 10p gain mutation analysis
D19V1, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                2                 23
  CLUS_2                0                 20
  CLUS_3                3                 21
D19V2, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                3                 21
  CLUS_3                1                 25
D19V3, multiclass
D19V4, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                0                 26
  CLUS_2                1                 37
  CLUS_3                2                 27
D19V5, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                4                 49
  CLUS_2                0                 33
  CLUS_3                4                 36
D19V6, multiclass
D19V7, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                0                 17
  CLUS_3                4                 12
  CLUS_4                0                 20
D19V8, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                0                 24
  CLUS_3                4                 26
D19V9, multiclass
D19V10, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                4                 59
  CLUS_3                2                 57

Clustering(20) Variable = 10q gain mutation analysis
D20V1, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 67 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-3913         TCGA-AG-3574         TCGA-AG-3575 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3609 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3611         TCGA-AG-3612         TCGA-AG-3726 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3878 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3881         TCGA-AG-3882         TCGA-AG-3883 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-3909         TCGA-AG-4001 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-4005         TCGA-AG-4007         TCGA-AG-4008 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-4015         TCGA-AG-A002         TCGA-AG-A008 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A00C         TCGA-AG-A00H         TCGA-AG-A00Y 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A011         TCGA-AG-A014         TCGA-AG-A015 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01J         TCGA-AG-A01L 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01N         TCGA-AG-A023         TCGA-AG-A025 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A026         TCGA-AG-A02G         TCGA-AG-A02X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A032 
"10Q GAIN WILD-TYPE" 
D20V2, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 67 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-3913         TCGA-AG-3574         TCGA-AG-3575 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3609 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3611         TCGA-AG-3612         TCGA-AG-3726 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3878 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3881         TCGA-AG-3882         TCGA-AG-3883 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-3909         TCGA-AG-4001 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-4005         TCGA-AG-4007         TCGA-AG-4008 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-4015         TCGA-AG-A002         TCGA-AG-A008 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A00C         TCGA-AG-A00H         TCGA-AG-A00Y 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A011         TCGA-AG-A014         TCGA-AG-A015 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01J         TCGA-AG-A01L 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01N         TCGA-AG-A023         TCGA-AG-A025 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A026         TCGA-AG-A02G         TCGA-AG-A02X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A032 
"10Q GAIN WILD-TYPE" 
D20V3, multiclass
D20V4, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 91 
        TCGA-AF-2687         TCGA-AF-2690         TCGA-AF-2693 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-3911         TCGA-AF-4110         TCGA-AF-6136 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3591 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3592         TCGA-AG-3725         TCGA-AG-3731 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3732         TCGA-AG-3742         TCGA-AG-4021 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-4022         TCGA-AG-A01Y         TCGA-AG-A020 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A026         TCGA-AG-A02N         TCGA-AH-6544 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6547         TCGA-AH-6643         TCGA-AH-6644 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6897         TCGA-AH-6903         TCGA-BM-6198 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CI-6619         TCGA-CI-6620         TCGA-CI-6621 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-4749         TCGA-DC-5337         TCGA-DC-5869 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6154         TCGA-DC-6155         TCGA-DC-6156 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DE         TCGA-DY-A1DF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DG         TCGA-DY-A1H8         TCGA-EF-5830 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EF-5831         TCGA-EI-6506         TCGA-EI-6507 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6508         TCGA-EI-6509         TCGA-EI-6510 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6511         TCGA-EI-6512         TCGA-EI-6513 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6514         TCGA-EI-6881         TCGA-EI-6882 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6883         TCGA-EI-6884         TCGA-EI-6885 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6917         TCGA-EI-7002         TCGA-EI-7004 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"10Q GAIN WILD-TYPE" 
D20V5, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                 51
  CLUS_2                0                 33
  CLUS_3                1                 39
D20V6, multiclass
D20V7, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 69 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-3913         TCGA-AG-3574         TCGA-AG-3575 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3609 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3611         TCGA-AG-3612         TCGA-AG-3726 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3878 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3881         TCGA-AG-3882         TCGA-AG-3883 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3909         TCGA-AG-4001         TCGA-AG-4005 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4015 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D20V8, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 69 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-3913         TCGA-AG-3574         TCGA-AG-3575 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3609 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3611         TCGA-AG-3612         TCGA-AG-3726 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3878 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3881         TCGA-AG-3882         TCGA-AG-3883 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3909         TCGA-AG-4001         TCGA-AG-4005 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4015 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D20V9, multiclass
D20V10, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                3                 60
  CLUS_3                1                 58

Clustering(21) Variable = 11p gain mutation analysis
D21V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 25
  CLUS_2                3                 17
  CLUS_3                5                 19
D21V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                 16
  CLUS_2                0                 24
  CLUS_3                5                 21
D21V3, multiclass
D21V4, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                6                 20
  CLUS_2                4                 34
  CLUS_3                3                 26
D21V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                8                 45
  CLUS_2                4                 29
  CLUS_3                4                 36
D21V6, multiclass
D21V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                4                 13
  CLUS_3                3                 13
  CLUS_4                1                 19
D21V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                2                 22
  CLUS_3                6                 24
D21V9, multiclass
D21V10, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                8                 55
  CLUS_3               10                 49

Clustering(22) Variable = 11q gain mutation analysis
D22V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 25
  CLUS_2                2                 18
  CLUS_3                4                 20
D22V2, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                 16
  CLUS_2                0                 24
  CLUS_3                3                 23
D22V3, multiclass
D22V4, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                7                 19
  CLUS_2                3                 35
  CLUS_3                1                 28
D22V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                6                 47
  CLUS_2                3                 30
  CLUS_3                2                 38
D22V6, multiclass
D22V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                5                 12
  CLUS_3                1                 15
  CLUS_4                0                 20
D22V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                1                 23
  CLUS_3                5                 25
D22V9, multiclass
D22V10, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                6                 57
  CLUS_3                7                 52

Clustering(23) Variable = 12p gain mutation analysis
D23V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                5                 20
  CLUS_2                6                 14
  CLUS_3                4                 20
D23V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                6                 18
  CLUS_3                7                 19
D23V3, multiclass
D23V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                4                 22
  CLUS_2                4                 34
  CLUS_3                4                 25
D23V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               12                 41
  CLUS_2                5                 28
  CLUS_3                4                 36
D23V6, multiclass
D23V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                3                 14
  CLUS_3                6                 10
  CLUS_4                6                 14
D23V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                8                 16
  CLUS_3                8                 22
D23V9, multiclass
D23V10, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2               15                 48
  CLUS_3                9                 50

Clustering(24) Variable = 12q gain mutation analysis
D24V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                 22
  CLUS_2                3                 17
  CLUS_3                3                 21
D24V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                3                 21
  CLUS_3                4                 22
D24V3, multiclass
D24V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                 23
  CLUS_2                2                 36
  CLUS_3                4                 25
D24V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                9                 44
  CLUS_2                5                 28
  CLUS_3                3                 37
D24V6, multiclass
D24V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                3                 14
  CLUS_3                3                 13
  CLUS_4                3                 17
D24V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                5                 19
  CLUS_3                5                 25
D24V9, multiclass
D24V10, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2               10                 53
  CLUS_3                6                 53

Clustering(25) Variable = 13q gain mutation analysis
D25V1, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               16                  9
  CLUS_2                9                 11
  CLUS_3               17                  7
D25V2, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               13                  6
  CLUS_2               17                  7
  CLUS_3               12                 14
D25V3, multiclass
D25V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               19                  7
  CLUS_2               26                 12
  CLUS_3               16                 13
D25V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               35                 18
  CLUS_2               19                 14
  CLUS_3               23                 17
D25V6, multiclass
D25V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               13                  5
  CLUS_2               11                  6
  CLUS_3               10                  6
  CLUS_4                7                 13
D25V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               12                  5
  CLUS_2                8                 16
  CLUS_3               21                  9
D25V9, multiclass
D25V10, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               11                  8
  CLUS_2               36                 27
  CLUS_3               44                 15

Clustering(26) Variable = 14q gain mutation analysis
D26V1, multiclass
D26V2, multiclass
D26V3, multiclass
D26V4, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                 24
  CLUS_2                0                 38
  CLUS_3                2                 27
D26V5, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                3                 50
  CLUS_2                0                 33
  CLUS_3                1                 39
D26V6, multiclass
D26V7, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 70 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-3913         TCGA-AG-3574         TCGA-AG-3575 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3609 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3611         TCGA-AG-3612         TCGA-AG-3726 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3878 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3881         TCGA-AG-3882         TCGA-AG-3883 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3909         TCGA-AG-3999         TCGA-AG-4001 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-4005         TCGA-AG-4007         TCGA-AG-4008 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-4015         TCGA-AG-A002         TCGA-AG-A008 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A00C         TCGA-AG-A00H         TCGA-AG-A00Y 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A011         TCGA-AG-A014         TCGA-AG-A015 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01J         TCGA-AG-A01L 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01N         TCGA-AG-A01W         TCGA-AG-A020 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A032 
"14Q GAIN WILD-TYPE" 
D26V8, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 70 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-3913         TCGA-AG-3574         TCGA-AG-3575 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3609 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3611         TCGA-AG-3612         TCGA-AG-3726 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3878 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3881         TCGA-AG-3882         TCGA-AG-3883 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3909         TCGA-AG-3999         TCGA-AG-4001 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-4005         TCGA-AG-4007         TCGA-AG-4008 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-4015         TCGA-AG-A002         TCGA-AG-A008 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A00C         TCGA-AG-A00H         TCGA-AG-A00Y 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A011         TCGA-AG-A014         TCGA-AG-A015 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01J         TCGA-AG-A01L 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01N         TCGA-AG-A01W         TCGA-AG-A020 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A032 
"14Q GAIN WILD-TYPE" 
D26V9, multiclass
D26V10, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                0                 63
  CLUS_3                2                 57

Clustering(27) Variable = 16p gain mutation analysis
D27V1, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                5                 20
  CLUS_2                1                 19
  CLUS_3                5                 19
D27V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                4                 15
  CLUS_2                5                 19
  CLUS_3                2                 24
D27V3, multiclass
D27V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                6                 20
  CLUS_2                5                 33
  CLUS_3                7                 22
D27V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                9                 44
  CLUS_2                5                 28
  CLUS_3                6                 34
D27V6, multiclass
D27V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                 16
  CLUS_3                4                 12
  CLUS_4                2                 18
D27V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 15
  CLUS_2                2                 22
  CLUS_3                6                 24
D27V9, multiclass
D27V10, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                9                 54
  CLUS_3               14                 45

Clustering(28) Variable = 16q gain mutation analysis
D28V1, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                 21
  CLUS_2                1                 19
  CLUS_3                5                 19
D28V2, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                 15
  CLUS_2                4                 20
  CLUS_3                2                 24
D28V3, multiclass
D28V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                7                 19
  CLUS_2                6                 32
  CLUS_3                7                 22
D28V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               11                 42
  CLUS_2                6                 27
  CLUS_3                6                 34
D28V6, multiclass
D28V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                 16
  CLUS_3                3                 13
  CLUS_4                2                 18
D28V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 15
  CLUS_2                2                 22
  CLUS_3                5                 25
D28V9, multiclass
D28V10, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                8                 55
  CLUS_3               16                 43

Clustering(29) Variable = 17p gain mutation analysis
D29V1, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 68 
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AG-3574 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3575         TCGA-AG-3578         TCGA-AG-3580 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3584         TCGA-AG-3586         TCGA-AG-3587 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3593         TCGA-AG-3594         TCGA-AG-3598 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3600         TCGA-AG-3601 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3602         TCGA-AG-3605         TCGA-AG-3608 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3611         TCGA-AG-3612         TCGA-AG-3726 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3878 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3881         TCGA-AG-3882         TCGA-AG-3883 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-3909         TCGA-AG-3999 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-A002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A023 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02X         TCGA-AG-A032 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D29V2, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 68 
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AG-3574 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3575         TCGA-AG-3578         TCGA-AG-3580 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3584         TCGA-AG-3586         TCGA-AG-3587 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3593         TCGA-AG-3594         TCGA-AG-3598 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3600         TCGA-AG-3601 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3602         TCGA-AG-3605         TCGA-AG-3608 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3611         TCGA-AG-3612         TCGA-AG-3726 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3878 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3881         TCGA-AG-3882         TCGA-AG-3883 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-3909         TCGA-AG-3999 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-A002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A023 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02X         TCGA-AG-A032 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D29V3, multiclass
D29V4, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 91 
        TCGA-AF-2687         TCGA-AF-2690         TCGA-AF-2693 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-3911         TCGA-AF-4110         TCGA-AF-6136 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3591 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3592         TCGA-AG-3725         TCGA-AG-3731 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3732         TCGA-AG-3742         TCGA-AG-4021 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4022         TCGA-AG-A01W         TCGA-AG-A01Y 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A026         TCGA-AG-A02N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6621         TCGA-CI-6622         TCGA-CI-6624 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6155         TCGA-DC-6156 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DE         TCGA-DY-A1DF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DG         TCGA-DY-A1H8         TCGA-EF-5830 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EF-5831         TCGA-EI-6506         TCGA-EI-6507 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6508         TCGA-EI-6509         TCGA-EI-6510 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6511         TCGA-EI-6512         TCGA-EI-6513 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6514         TCGA-EI-6881         TCGA-EI-6882 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6883         TCGA-EI-6884         TCGA-EI-6885 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6917         TCGA-EI-7002         TCGA-EI-7004 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"17P GAIN WILD-TYPE" 
D29V5, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                125 
        TCGA-AF-2689         TCGA-AF-2690         TCGA-AF-3400 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-3913         TCGA-AF-5654         TCGA-AF-6136 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3574 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3591 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3593         TCGA-AG-3594         TCGA-AG-3598 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3600         TCGA-AG-3601 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3602         TCGA-AG-3605         TCGA-AG-3612 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3725         TCGA-AG-3727         TCGA-AG-3731 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3742         TCGA-AG-3878         TCGA-AG-3881 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3882         TCGA-AG-3885         TCGA-AG-3893 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-4001         TCGA-AG-4005 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4015 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4021         TCGA-AG-4022         TCGA-AG-A002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01N         TCGA-AG-A01W         TCGA-AG-A01Y 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A023         TCGA-AG-A026 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-BM-6198 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6621         TCGA-CL-5918         TCGA-DC-4745 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-4749         TCGA-DC-5337         TCGA-DC-5869 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6884 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-F5-6464 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6465         TCGA-F5-6571         TCGA-F5-6702 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6810         TCGA-F5-6811         TCGA-F5-6812 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6813         TCGA-F5-6861         TCGA-F5-6863 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D29V6, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                125 
        TCGA-AF-2689         TCGA-AF-2690         TCGA-AF-3400 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-3913         TCGA-AF-5654         TCGA-AF-6136 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3574 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3591 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3593         TCGA-AG-3594         TCGA-AG-3598 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3600         TCGA-AG-3601 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3602         TCGA-AG-3605         TCGA-AG-3612 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3725         TCGA-AG-3727         TCGA-AG-3731 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3742         TCGA-AG-3878         TCGA-AG-3881 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3882         TCGA-AG-3885         TCGA-AG-3893 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-4001         TCGA-AG-4005 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4015 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4021         TCGA-AG-4022         TCGA-AG-A002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01N         TCGA-AG-A01W         TCGA-AG-A01Y 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A023         TCGA-AG-A026 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-BM-6198 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6621         TCGA-CL-5918         TCGA-DC-4745 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-4749         TCGA-DC-5337         TCGA-DC-5869 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6884 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-F5-6464 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6465         TCGA-F5-6571         TCGA-F5-6702 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6810         TCGA-F5-6811         TCGA-F5-6812 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6813         TCGA-F5-6861         TCGA-F5-6863 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D29V7, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 70 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-3913         TCGA-AG-3574         TCGA-AG-3575 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3611 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3612         TCGA-AG-3726         TCGA-AG-3727 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3728         TCGA-AG-3878         TCGA-AG-3881 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3882         TCGA-AG-3883         TCGA-AG-3885 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3890         TCGA-AG-3892 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3898         TCGA-AG-3901         TCGA-AG-3909 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4005 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4015 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A032 
"17P GAIN WILD-TYPE" 
D29V8, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 70 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-3913         TCGA-AG-3574         TCGA-AG-3575 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3611 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3612         TCGA-AG-3726         TCGA-AG-3727 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3728         TCGA-AG-3878         TCGA-AG-3881 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3882         TCGA-AG-3883         TCGA-AG-3885 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3890         TCGA-AG-3892 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3898         TCGA-AG-3901         TCGA-AG-3909 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4005 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4015 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A032 
"17P GAIN WILD-TYPE" 
D29V9, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                139 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3574 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3575         TCGA-AG-3578         TCGA-AG-3580 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3584         TCGA-AG-3586         TCGA-AG-3587 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3591         TCGA-AG-3592         TCGA-AG-3593 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3611 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3612         TCGA-AG-3725         TCGA-AG-3726 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3731 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3732         TCGA-AG-3742         TCGA-AG-3878 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3881         TCGA-AG-3882         TCGA-AG-3883 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-3909         TCGA-AG-3999 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-4021 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4022         TCGA-AG-A002         TCGA-AG-A008 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00C         TCGA-AG-A011         TCGA-AG-A015 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01L         TCGA-AG-A01N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AH-6544 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6547         TCGA-AH-6643         TCGA-AH-6644 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6621         TCGA-CI-6622         TCGA-CI-6624 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6155         TCGA-DC-6156 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DE         TCGA-DY-A1DF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DG         TCGA-DY-A1H8         TCGA-EF-5830 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EF-5831         TCGA-EI-6506         TCGA-EI-6507 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6508         TCGA-EI-6509         TCGA-EI-6510 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6511         TCGA-EI-6512         TCGA-EI-6513 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6514         TCGA-F5-6464         TCGA-F5-6465 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"17P GAIN WILD-TYPE" 
D29V10, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                139 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3574 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3575         TCGA-AG-3578         TCGA-AG-3580 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3584         TCGA-AG-3586         TCGA-AG-3587 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3591         TCGA-AG-3592         TCGA-AG-3593 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3611 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3612         TCGA-AG-3725         TCGA-AG-3726 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3731 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3732         TCGA-AG-3742         TCGA-AG-3878 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3881         TCGA-AG-3882         TCGA-AG-3883 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-3909         TCGA-AG-3999 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-4021 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4022         TCGA-AG-A002         TCGA-AG-A008 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00C         TCGA-AG-A011         TCGA-AG-A015 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01L         TCGA-AG-A01N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AH-6544 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6547         TCGA-AH-6643         TCGA-AH-6644 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6621         TCGA-CI-6622         TCGA-CI-6624 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6155         TCGA-DC-6156 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DE         TCGA-DY-A1DF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DG         TCGA-DY-A1H8         TCGA-EF-5830 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EF-5831         TCGA-EI-6506         TCGA-EI-6507 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6508         TCGA-EI-6509         TCGA-EI-6510 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6511         TCGA-EI-6512         TCGA-EI-6513 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6514         TCGA-F5-6464         TCGA-F5-6465 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"17P GAIN WILD-TYPE" 

Clustering(30) Variable = 17q gain mutation analysis
D30V1, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 24
  CLUS_2                3                 17
  CLUS_3                5                 19
D30V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                2                 22
  CLUS_3                5                 21
D30V3, multiclass
D30V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                 23
  CLUS_2                3                 35
  CLUS_3                3                 26
D30V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                5                 48
  CLUS_2                4                 29
  CLUS_3                4                 36
D30V6, multiclass
D30V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                2                 15
  CLUS_3                5                 11
  CLUS_4                1                 19
D30V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 16
  CLUS_2                2                 22
  CLUS_3                6                 24
D30V9, multiclass
D30V10, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                8                 55
  CLUS_3                6                 53

Clustering(31) Variable = 18p gain mutation analysis
D31V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 24
  CLUS_2                2                 18
  CLUS_3                0                 24
D31V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                1                 23
  CLUS_3                2                 24
D31V3, multiclass
D31V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 25
  CLUS_2                3                 35
  CLUS_3                0                 29
D31V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                 49
  CLUS_2                1                 32
  CLUS_3                2                 38
D31V6, multiclass
D31V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                1                 16
  CLUS_3                1                 15
  CLUS_4                2                 18
D31V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                2                 22
  CLUS_3                2                 28
D31V9, multiclass
D31V10, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                3                 60
  CLUS_3                3                 56

Clustering(32) Variable = 18q gain mutation analysis
D32V1, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 68 
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AG-3574 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3575         TCGA-AG-3578         TCGA-AG-3580 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3584         TCGA-AG-3586         TCGA-AG-3587 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3593         TCGA-AG-3594         TCGA-AG-3598 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3600         TCGA-AG-3601 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3602         TCGA-AG-3605         TCGA-AG-3608 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3609         TCGA-AG-3611         TCGA-AG-3612 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3726         TCGA-AG-3727         TCGA-AG-3728 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3878         TCGA-AG-3881         TCGA-AG-3882 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3885         TCGA-AG-3887 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3890         TCGA-AG-3892         TCGA-AG-3893 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3896         TCGA-AG-3898 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3901         TCGA-AG-3902         TCGA-AG-3909 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4005 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4015 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A02X         TCGA-AG-A032 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D32V2, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 68 
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AG-3574 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3575         TCGA-AG-3578         TCGA-AG-3580 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3584         TCGA-AG-3586         TCGA-AG-3587 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3593         TCGA-AG-3594         TCGA-AG-3598 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3600         TCGA-AG-3601 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3602         TCGA-AG-3605         TCGA-AG-3608 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3609         TCGA-AG-3611         TCGA-AG-3612 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3726         TCGA-AG-3727         TCGA-AG-3728 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3878         TCGA-AG-3881         TCGA-AG-3882 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3885         TCGA-AG-3887 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3890         TCGA-AG-3892         TCGA-AG-3893 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3896         TCGA-AG-3898 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3901         TCGA-AG-3902         TCGA-AG-3909 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4005 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4015 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A02X         TCGA-AG-A032 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D32V3, multiclass
D32V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 26
  CLUS_2                3                 35
  CLUS_3                0                 29
D32V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                 51
  CLUS_2                1                 32
  CLUS_3                1                 39
D32V6, multiclass
D32V7, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 70 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-3913         TCGA-AG-3574         TCGA-AG-3575 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3609 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3611         TCGA-AG-3612         TCGA-AG-3726 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3878 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3881         TCGA-AG-3882         TCGA-AG-3883 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3909         TCGA-AG-3999         TCGA-AG-4001 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4005         TCGA-AG-4007         TCGA-AG-4008 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4015         TCGA-AG-A002         TCGA-AG-A008 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A00C         TCGA-AG-A00H         TCGA-AG-A00Y 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A011         TCGA-AG-A014         TCGA-AG-A015 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01J         TCGA-AG-A01L 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01N         TCGA-AG-A01W         TCGA-AG-A01Y 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A023         TCGA-AG-A025 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A026         TCGA-AG-A02N         TCGA-AG-A02X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A032 
"18Q GAIN WILD-TYPE" 
D32V8, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 70 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-3913         TCGA-AG-3574         TCGA-AG-3575 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3609 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3611         TCGA-AG-3612         TCGA-AG-3726 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3878 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3881         TCGA-AG-3882         TCGA-AG-3883 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3909         TCGA-AG-3999         TCGA-AG-4001 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4005         TCGA-AG-4007         TCGA-AG-4008 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4015         TCGA-AG-A002         TCGA-AG-A008 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A00C         TCGA-AG-A00H         TCGA-AG-A00Y 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A011         TCGA-AG-A014         TCGA-AG-A015 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01J         TCGA-AG-A01L 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01N         TCGA-AG-A01W         TCGA-AG-A01Y 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A023         TCGA-AG-A025 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A026         TCGA-AG-A02N         TCGA-AG-A02X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A032 
"18Q GAIN WILD-TYPE" 
D32V9, multiclass
D32V10, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                1                 62
  CLUS_3                3                 56

Clustering(33) Variable = 19p gain mutation analysis
D33V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 25
  CLUS_2                4                 16
  CLUS_3                7                 17
D33V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                5                 14
  CLUS_2                1                 23
  CLUS_3                5                 21
D33V3, multiclass
D33V4, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                3                 23
  CLUS_2                3                 35
  CLUS_3                4                 25
D33V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                8                 45
  CLUS_2                4                 29
  CLUS_3                5                 35
D33V6, multiclass
D33V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                2                 15
  CLUS_3                6                 10
  CLUS_4                1                 19
D33V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 16
  CLUS_2                2                 22
  CLUS_3                8                 22
D33V9, multiclass
D33V10, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                9                 54
  CLUS_3                7                 52

Clustering(34) Variable = 19q gain mutation analysis
D34V1, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 23
  CLUS_2                2                 18
  CLUS_3                9                 15
D34V2, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                7                 12
  CLUS_2                3                 21
  CLUS_3                3                 23
D34V3, multiclass
D34V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                4                 22
  CLUS_2                3                 35
  CLUS_3                4                 25
D34V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               10                 43
  CLUS_2                3                 30
  CLUS_3                5                 35
D34V6, multiclass
D34V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                2                 15
  CLUS_3                8                  8
  CLUS_4                1                 19
D34V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 16
  CLUS_2                2                 22
  CLUS_3               10                 20
D34V9, multiclass
D34V10, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 17
  CLUS_2               10                 53
  CLUS_3                7                 52

Clustering(35) Variable = 20p gain mutation analysis
D35V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               14                 11
  CLUS_2               10                 10
  CLUS_3               15                  9
D35V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               13                  6
  CLUS_2               13                 11
  CLUS_3               13                 13
D35V3, multiclass
D35V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               17                  9
  CLUS_2               23                 15
  CLUS_3               15                 14
D35V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               35                 18
  CLUS_2               21                 12
  CLUS_3               16                 24
D35V6, multiclass
D35V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               10                  8
  CLUS_2               11                  6
  CLUS_3                7                  9
  CLUS_4               10                 10
D35V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               12                  5
  CLUS_2                8                 16
  CLUS_3               18                 12
D35V9, multiclass
D35V10, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               10                  9
  CLUS_2               33                 30
  CLUS_3               40                 19

Clustering(36) Variable = 20q gain mutation analysis
D36V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               21                  4
  CLUS_2               13                  7
  CLUS_3               22                  2
D36V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               18                  1
  CLUS_2               20                  4
  CLUS_3               18                  8
D36V3, multiclass
D36V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               24                  2
  CLUS_2               30                  8
  CLUS_3               22                  7
D36V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               47                  6
  CLUS_2               25                  8
  CLUS_3               32                  8
D36V6, multiclass
D36V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               15                  3
  CLUS_2               12                  5
  CLUS_3               16                  0
  CLUS_4               13                  7
D36V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               16                  1
  CLUS_2               11                 13
  CLUS_3               29                  1
D36V9, multiclass
D36V10, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               16                  3
  CLUS_2               49                 14
  CLUS_3               51                  8

Clustering(37) Variable = 21q gain mutation analysis
D37V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 23
  CLUS_2                1                 19
  CLUS_3                0                 24
D37V2, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 24
  CLUS_3                3                 23
D37V3, multiclass
D37V4, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 25
  CLUS_2                1                 37
  CLUS_3                2                 27
D37V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 51
  CLUS_2                1                 32
  CLUS_3                2                 38
D37V6, multiclass
D37V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                0                 17
  CLUS_3                0                 16
  CLUS_4                1                 19
D37V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 16
  CLUS_2                1                 23
  CLUS_3                1                 29
D37V9, multiclass
D37V10, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                3                 60
  CLUS_3                2                 57

Clustering(38) Variable = 22q gain mutation analysis
D38V1, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                 25
  CLUS_2                2                 18
  CLUS_3                1                 23
D38V2, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                0                 24
  CLUS_3                3                 23
D38V3, multiclass
D38V4, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 91 
        TCGA-AF-2687         TCGA-AF-2690         TCGA-AF-2693 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AF-3911         TCGA-AF-4110         TCGA-AF-6136 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3591 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3592         TCGA-AG-3725         TCGA-AG-3731 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3732         TCGA-AG-3742         TCGA-AG-4021 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-4022         TCGA-AG-A01W         TCGA-AG-A01Y 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A026         TCGA-AG-A02N 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6903         TCGA-BM-6198 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CI-6619         TCGA-CI-6620         TCGA-CI-6621 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DG         TCGA-DY-A1H8         TCGA-EF-5830 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EF-5831         TCGA-EI-6506         TCGA-EI-6507 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6508         TCGA-EI-6509         TCGA-EI-6510 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6511         TCGA-EI-6512         TCGA-EI-6513 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6514         TCGA-EI-6881         TCGA-EI-6882 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6883         TCGA-EI-6884         TCGA-EI-6885 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6917         TCGA-EI-7002         TCGA-EI-7004 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"22Q GAIN WILD-TYPE" 
D38V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                2                 51
  CLUS_2                2                 31
  CLUS_3                1                 39
D38V6, multiclass
D38V7, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                2                 15
  CLUS_3                1                 15
  CLUS_4                0                 20
D38V8, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                0                 24
  CLUS_3                3                 27
D38V9, multiclass
D38V10, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                3                 60
  CLUS_3                1                 58

Clustering(39) Variable = Xq gain mutation analysis
D39V1, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                23
  CLUS_2               1                19
  CLUS_3               1                23
D39V2, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                18
  CLUS_2               2                22
  CLUS_3               1                25
D39V3, multiclass
D39V4, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                25
  CLUS_2               1                37
  CLUS_3               1                28
D39V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3                50
  CLUS_2               2                31
  CLUS_3               1                39
D39V6, multiclass
D39V7, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                18
  CLUS_2               1                16
  CLUS_3               1                15
  CLUS_4               2                18
D39V8, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                17
  CLUS_2               2                22
  CLUS_3               2                28
D39V9, multiclass
D39V10, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                19
  CLUS_2               4                59
  CLUS_3               3                56

Clustering(40) Variable = 1p loss mutation analysis
D40V1, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3                22
  CLUS_2               4                16
  CLUS_3               2                22
D40V2, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2                17
  CLUS_2               3                21
  CLUS_3               4                22
D40V3, multiclass
D40V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3                23
  CLUS_2               7                31
  CLUS_3               2                27
D40V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               6                47
  CLUS_2               2                31
  CLUS_3               7                33
D40V6, multiclass
D40V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               4                14
  CLUS_2               2                15
  CLUS_3               3                13
  CLUS_4               0                20
D40V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3                14
  CLUS_2               1                23
  CLUS_3               5                25
D40V9, multiclass
D40V10, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               8                55
  CLUS_3              10                49

Clustering(41) Variable = 1q loss mutation analysis
D41V1, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               1                24
  CLUS_2               1                19
  CLUS_3               2                22
D41V2, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2                17
  CLUS_2               1                23
  CLUS_3               1                25
D41V3, multiclass
D41V4, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               1                25
  CLUS_2               2                36
  CLUS_3               0                29
D41V5, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2                51
  CLUS_2               0                33
  CLUS_3               2                38
D41V6, multiclass
D41V7, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               1                16
  CLUS_3               0                16
  CLUS_4               0                20
D41V8, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3                14
  CLUS_2               0                24
  CLUS_3               1                29
D41V9, multiclass
D41V10, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               4                59
  CLUS_3               3                56

Clustering(42) Variable = 2p loss mutation analysis
D42V1, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                24
  CLUS_2               3                17
  CLUS_3               1                23
D42V2, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               1                23
  CLUS_3               3                23
D42V3, multiclass
D42V4, multiclass
D42V5, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                52
  CLUS_2               2                31
  CLUS_3               1                39
D42V6, multiclass
D42V7, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               3                14
  CLUS_3               0                16
  CLUS_4               2                18
D42V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                17
  CLUS_2               3                21
  CLUS_3               2                28
D42V9, multiclass
D42V10, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               5                58
  CLUS_3               0                59

Clustering(43) Variable = 3p loss mutation analysis
D43V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                23
  CLUS_2               1                19
  CLUS_3               1                23
D43V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               1                23
  CLUS_3               2                24
D43V3, multiclass
D43V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                26
  CLUS_2               3                35
  CLUS_3               1                28
D43V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               4                49
  CLUS_2               2                31
  CLUS_3               2                38
D43V6, multiclass
D43V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               1                16
  CLUS_3               0                16
  CLUS_4               1                19
D43V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                16
  CLUS_2               2                22
  CLUS_3               1                29
D43V9, multiclass
D43V10, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               4                59
  CLUS_3               4                55

Clustering(44) Variable = 3q loss mutation analysis
D44V1, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                67 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3580 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3584        TCGA-AG-3586 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3587        TCGA-AG-3593        TCGA-AG-3594        TCGA-AG-3598 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3600        TCGA-AG-3601        TCGA-AG-3602 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3605        TCGA-AG-3608        TCGA-AG-3609        TCGA-AG-3611 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3612        TCGA-AG-3726        TCGA-AG-3727        TCGA-AG-3728 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882        TCGA-AG-3883 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890        TCGA-AG-3892 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3901        TCGA-AG-3902        TCGA-AG-3909        TCGA-AG-3999 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-4001        TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-4015        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02X        TCGA-AG-A032 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D44V2, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                67 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3580 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3584        TCGA-AG-3586 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3587        TCGA-AG-3593        TCGA-AG-3594        TCGA-AG-3598 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3600        TCGA-AG-3601        TCGA-AG-3602 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3605        TCGA-AG-3608        TCGA-AG-3609        TCGA-AG-3611 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3612        TCGA-AG-3726        TCGA-AG-3727        TCGA-AG-3728 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882        TCGA-AG-3883 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890        TCGA-AG-3892 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3901        TCGA-AG-3902        TCGA-AG-3909        TCGA-AG-3999 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-4001        TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-4015        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02X        TCGA-AG-A032 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D44V3, multiclass
D44V4, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                91 
       TCGA-AF-2687        TCGA-AF-2690        TCGA-AF-2693        TCGA-AF-3911 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-4110        TCGA-AF-6136        TCGA-AF-6655        TCGA-AF-6672 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3591        TCGA-AG-3592        TCGA-AG-3725        TCGA-AG-3731 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3732        TCGA-AG-3742        TCGA-AG-4021        TCGA-AG-4022 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A026 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6644        TCGA-AH-6897        TCGA-AH-6903        TCGA-CI-6619 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6621        TCGA-CI-6622        TCGA-CI-6623 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CI-6624        TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-4745        TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6154        TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6683        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6464 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6861        TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6572        TCGA-G5-6641 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D44V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                51
  CLUS_2               1                32
  CLUS_3               1                39
D44V6, multiclass
D44V7, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                69 
       TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400        TCGA-AF-3913 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3580        TCGA-AG-3581 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3593        TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3600        TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3608        TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3726        TCGA-AG-3727        TCGA-AG-3728        TCGA-AG-3878 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3881        TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3885 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3890        TCGA-AG-3892        TCGA-AG-3893 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898        TCGA-AG-3901 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4005 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A002 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A01J        TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A032 
"3Q LOSS WILD-TYPE" 
D44V8, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                69 
       TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400        TCGA-AF-3913 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3580        TCGA-AG-3581 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3593        TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3600        TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3608        TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3726        TCGA-AG-3727        TCGA-AG-3728        TCGA-AG-3878 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3881        TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3885 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3890        TCGA-AG-3892        TCGA-AG-3893 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898        TCGA-AG-3901 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4005 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A002 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A01J        TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A032 
"3Q LOSS WILD-TYPE" 
D44V9, multiclass
D44V10, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               2                61
  CLUS_3               2                57

Clustering(45) Variable = 4p loss mutation analysis
D45V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               6                19
  CLUS_2               7                13
  CLUS_3               4                20
D45V2, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               4                15
  CLUS_2               6                18
  CLUS_3               7                19
D45V3, multiclass
D45V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               7                19
  CLUS_2               8                30
  CLUS_3               7                22
D45V5, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              13                40
  CLUS_2               5                28
  CLUS_3              10                30
D45V6, multiclass
D45V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               7                10
  CLUS_3               4                12
  CLUS_4               4                16
D45V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               3                14
  CLUS_2               5                19
  CLUS_3              10                20
D45V9, multiclass
D45V10, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               5                14
  CLUS_2              15                48
  CLUS_3              15                44

Clustering(46) Variable = 4q loss mutation analysis
D46V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               7                18
  CLUS_2               7                13
  CLUS_3               5                19
D46V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               5                14
  CLUS_2               7                17
  CLUS_3               7                19
D46V3, multiclass
D46V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               8                18
  CLUS_2              12                26
  CLUS_3               7                22
D46V5, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              13                40
  CLUS_2               7                26
  CLUS_3              13                27
D46V6, multiclass
D46V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               4                14
  CLUS_2               9                 8
  CLUS_3               4                12
  CLUS_4               4                16
D46V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               3                14
  CLUS_2               6                18
  CLUS_3              12                18
D46V9, multiclass
D46V10, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               6                13
  CLUS_2              17                46
  CLUS_3              19                40

Clustering(47) Variable = 5p loss mutation analysis
D47V1, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                25
  CLUS_2               3                17
  CLUS_3               2                22
D47V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2                17
  CLUS_2               0                24
  CLUS_3               3                23
D47V3, multiclass
D47V4, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                23
  CLUS_2               1                37
  CLUS_3               2                27
D47V5, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               5                48
  CLUS_2               1                32
  CLUS_3               2                38
D47V6, multiclass
D47V7, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               1                16
  CLUS_3               3                13
  CLUS_4               2                18
D47V8, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                17
  CLUS_2               2                22
  CLUS_3               4                26
D47V9, multiclass
D47V10, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                16
  CLUS_2               5                58
  CLUS_3               2                57

Clustering(48) Variable = 5q loss mutation analysis
D48V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                25
  CLUS_2               5                15
  CLUS_3               3                21
D48V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3                16
  CLUS_2               0                24
  CLUS_3               5                21
D48V3, multiclass
D48V4, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               8                18
  CLUS_2               4                34
  CLUS_3               4                25
D48V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               8                45
  CLUS_2               4                29
  CLUS_3               5                35
D48V6, multiclass
D48V7, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               3                14
  CLUS_3               4                12
  CLUS_4               2                18
D48V8, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                17
  CLUS_2               3                21
  CLUS_3               7                23
D48V9, multiclass
D48V10, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               6                13
  CLUS_2               8                55
  CLUS_3               9                50

Clustering(49) Variable = 6p loss mutation analysis
D49V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3                22
  CLUS_2               0                20
  CLUS_3               1                23
D49V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               2                22
  CLUS_3               1                25
D49V3, multiclass
D49V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                26
  CLUS_2               0                38
  CLUS_3               4                25
D49V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3                50
  CLUS_2               1                32
  CLUS_3               2                38
D49V6, multiclass
D49V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               0                17
  CLUS_3               0                16
  CLUS_4               1                19
D49V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                15
  CLUS_2               2                22
  CLUS_3               0                30
D49V9, multiclass
D49V10, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               4                59
  CLUS_3               3                56

Clustering(50) Variable = 6q loss mutation analysis
D50V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3                22
  CLUS_2               3                17
  CLUS_3               3                21
D50V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                17
  CLUS_2               2                22
  CLUS_3               5                21
D50V3, multiclass
D50V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                26
  CLUS_2               2                36
  CLUS_3               3                26
D50V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6                47
  CLUS_2               3                30
  CLUS_3               1                39
D50V6, multiclass
D50V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               4                14
  CLUS_2               2                15
  CLUS_3               0                16
  CLUS_4               3                17
D50V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3                14
  CLUS_2               6                18
  CLUS_3               0                30
D50V9, multiclass
D50V10, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               9                54
  CLUS_3               4                55

Clustering(51) Variable = 8p loss mutation analysis
D51V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               8                17
  CLUS_2               8                12
  CLUS_3              11                13
D51V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              10                 9
  CLUS_2               8                16
  CLUS_3               9                17
D51V3, multiclass
D51V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               7                19
  CLUS_2              14                24
  CLUS_3               9                20
D51V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              19                34
  CLUS_2               9                24
  CLUS_3              12                28
D51V6, multiclass
D51V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               8                10
  CLUS_2               7                10
  CLUS_3               7                 9
  CLUS_4               5                15
D51V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               8                 9
  CLUS_2               6                18
  CLUS_3              13                17
D51V9, multiclass
D51V10, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               3                16
  CLUS_2              21                42
  CLUS_3              25                34

Clustering(52) Variable = 8q loss mutation analysis
D52V1, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                67 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3608        TCGA-AG-3609 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726        TCGA-AG-3727 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3728        TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3902        TCGA-AG-3909 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4005        TCGA-AG-4007 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A002        TCGA-AG-A008 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A023        TCGA-AG-A025 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A032 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D52V2, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                67 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3608        TCGA-AG-3609 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726        TCGA-AG-3727 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3728        TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3883        TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3902        TCGA-AG-3909 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4005        TCGA-AG-4007 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A002        TCGA-AG-A008 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A023        TCGA-AG-A025 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A032 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D52V3, multiclass
D52V4, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                92 
       TCGA-AF-2687        TCGA-AF-2690        TCGA-AF-2693        TCGA-AF-3911 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-4110        TCGA-AF-6136        TCGA-AF-6655        TCGA-AF-6672 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3591        TCGA-AG-3592        TCGA-AG-3725        TCGA-AG-3731 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3732        TCGA-AG-3742        TCGA-AG-4021        TCGA-AG-4022 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A026 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6644        TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621        TCGA-CI-6622 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957        TCGA-CL-5917 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749        TCGA-DC-5337 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155        TCGA-DC-6156 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DY-A1DD        TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DY-A1H8        TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6511        TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6881        TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6885        TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863        TCGA-F5-6864 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572        TCGA-G5-6641 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D52V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2                51
  CLUS_2               0                33
  CLUS_3               1                39
D52V6, multiclass
D52V7, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                69 
       TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400        TCGA-AF-3913 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578        TCGA-AG-3580 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3584 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593        TCGA-AG-3594 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600        TCGA-AG-3601 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3602        TCGA-AG-3608        TCGA-AG-3609        TCGA-AG-3611 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3612        TCGA-AG-3726        TCGA-AG-3727        TCGA-AG-3728 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882        TCGA-AG-3883 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890        TCGA-AG-3892 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3901        TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L        TCGA-AG-A01N 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A023 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02N 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A032 
"8Q LOSS WILD-TYPE" 
D52V8, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                69 
       TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400        TCGA-AF-3913 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578        TCGA-AG-3580 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3584 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593        TCGA-AG-3594 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600        TCGA-AG-3601 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3602        TCGA-AG-3608        TCGA-AG-3609        TCGA-AG-3611 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3612        TCGA-AG-3726        TCGA-AG-3727        TCGA-AG-3728 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3878        TCGA-AG-3881        TCGA-AG-3882        TCGA-AG-3883 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890        TCGA-AG-3892 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3893        TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3901        TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L        TCGA-AG-A01N 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A023 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02N 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A032 
"8Q LOSS WILD-TYPE" 
D52V9, multiclass
D52V10, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               2                61
  CLUS_3               1                58

Clustering(53) Variable = 9p loss mutation analysis
D53V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               3                22
  CLUS_2               2                18
  CLUS_3               1                23
D53V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               3                21
  CLUS_3               2                24
D53V3, multiclass
D53V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               2                24
  CLUS_2               2                36
  CLUS_3               3                26
D53V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               6                47
  CLUS_2               1                32
  CLUS_3               4                36
D53V6, multiclass
D53V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               0                17
  CLUS_3               4                12
  CLUS_4               2                18
D53V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               0                17
  CLUS_2               2                22
  CLUS_3               4                26
D53V9, multiclass
D53V10, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               6                57
  CLUS_3               5                54

Clustering(54) Variable = 9q loss mutation analysis
D54V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               4                21
  CLUS_2               1                19
  CLUS_3               2                22
D54V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               2                17
  CLUS_2               4                20
  CLUS_3               1                25
D54V3, multiclass
D54V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                25
  CLUS_2               2                36
  CLUS_3               2                27
D54V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               4                49
  CLUS_2               1                32
  CLUS_3               4                36
D54V6, multiclass
D54V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               1                16
  CLUS_3               4                12
  CLUS_4               1                19
D54V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               0                17
  CLUS_2               2                22
  CLUS_3               5                25
D54V9, multiclass
D54V10, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               0                19
  CLUS_2               7                56
  CLUS_3               4                55

Clustering(55) Variable = 10p loss mutation analysis
D55V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                5                 20
  CLUS_2                0                 20
  CLUS_3                1                 23
D55V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                5                 19
  CLUS_3                0                 26
D55V3, multiclass
D55V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                4                 22
  CLUS_2                3                 35
  CLUS_3                4                 25
D55V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                9                 44
  CLUS_2                1                 32
  CLUS_3                3                 37
D55V6, multiclass
D55V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                0                 17
  CLUS_3                1                 15
  CLUS_4                4                 16
D55V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                 15
  CLUS_2                4                 20
  CLUS_3                1                 29
D55V9, multiclass
D55V10, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                7                 56
  CLUS_3                7                 52

Clustering(56) Variable = 10q loss mutation analysis
D56V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                6                 19
  CLUS_2                2                 18
  CLUS_3                1                 23
D56V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                5                 19
  CLUS_3                3                 23
D56V3, multiclass
D56V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                 21
  CLUS_2                4                 34
  CLUS_3                3                 26
D56V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               10                 43
  CLUS_2                3                 30
  CLUS_3                4                 36
D56V6, multiclass
D56V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                0                 17
  CLUS_3                1                 15
  CLUS_4                6                 14
D56V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                3                 14
  CLUS_2                6                 18
  CLUS_3                1                 29
D56V9, multiclass
D56V10, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                2                 17
  CLUS_2               10                 53
  CLUS_3                8                 51

Clustering(57) Variable = 11p loss mutation analysis
D57V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                4                 21
  CLUS_2                4                 16
  CLUS_3                0                 24
D57V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                3                 21
  CLUS_3                5                 21
D57V3, multiclass
D57V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                 26
  CLUS_2                5                 33
  CLUS_3                6                 23
D57V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                9                 44
  CLUS_2                3                 30
  CLUS_3                5                 35
D57V6, multiclass
D57V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                 16
  CLUS_3                0                 16
  CLUS_4                5                 15
D57V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                 15
  CLUS_2                6                 18
  CLUS_3                1                 29
D57V9, multiclass
D57V10, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                9                 54
  CLUS_3                9                 50

Clustering(58) Variable = 11q loss mutation analysis
D58V1, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                4                 21
  CLUS_2                4                 16
  CLUS_3                0                 24
D58V2, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                3                 21
  CLUS_3                5                 21
D58V3, multiclass
D58V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                 25
  CLUS_2                8                 30
  CLUS_3                6                 23
D58V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                8                 45
  CLUS_2                4                 29
  CLUS_3                6                 34
D58V6, multiclass
D58V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                1                 16
  CLUS_3                0                 16
  CLUS_4                4                 16
D58V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 15
  CLUS_2                6                 18
  CLUS_3                1                 29
D58V9, multiclass
D58V10, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                9                 54
  CLUS_3               13                 46

Clustering(59) Variable = 12p loss mutation analysis
D59V1, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 24
  CLUS_2                2                 18
  CLUS_3                2                 22
D59V2, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                1                 23
  CLUS_3                2                 24
D59V3, multiclass
D59V4, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 25
  CLUS_2                1                 37
  CLUS_3                5                 24
D59V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                6                 47
  CLUS_2                3                 30
  CLUS_3                2                 38
D59V6, multiclass
D59V7, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 16
  CLUS_3                3                 13
  CLUS_4                0                 20
D59V8, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                1                 23
  CLUS_3                5                 25
D59V9, multiclass
D59V10, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                3                 16
  CLUS_2                5                 58
  CLUS_3                4                 55

Clustering(60) Variable = 12q loss mutation analysis
D60V1, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                1                 24
  CLUS_2                1                 19
  CLUS_3                1                 23
D60V2, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                2                 22
  CLUS_3                1                 25
D60V3, multiclass
D60V4, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                1                 25
  CLUS_2                2                 36
  CLUS_3                2                 27
D60V5, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                4                 49
  CLUS_2                1                 32
  CLUS_3                2                 38
D60V6, multiclass
D60V7, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                0                 17
  CLUS_3                2                 14
  CLUS_4                0                 20
D60V8, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                0                 17
  CLUS_2                0                 24
  CLUS_3                3                 27
D60V9, multiclass
D60V10, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                2                 61
  CLUS_3                4                 55

Clustering(61) Variable = 13q loss mutation analysis
D61V1, multiclass
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 67 
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AG-3574 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3575         TCGA-AG-3578         TCGA-AG-3580 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3584         TCGA-AG-3586         TCGA-AG-3587 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3593         TCGA-AG-3598         TCGA-AG-3599 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3601         TCGA-AG-3602         TCGA-AG-3605 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3608         TCGA-AG-3609         TCGA-AG-3611 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3612         TCGA-AG-3726         TCGA-AG-3727 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3728         TCGA-AG-3878         TCGA-AG-3881 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3882         TCGA-AG-3883         TCGA-AG-3885 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3890         TCGA-AG-3892 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3898         TCGA-AG-3901         TCGA-AG-3902 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3909         TCGA-AG-3999         TCGA-AG-4001 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4005         TCGA-AG-4007         TCGA-AG-4008 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4015         TCGA-AG-A002         TCGA-AG-A008 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A00C         TCGA-AG-A00H         TCGA-AG-A00Y 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A011         TCGA-AG-A014         TCGA-AG-A015 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01J         TCGA-AG-A01L 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01N         TCGA-AG-A023         TCGA-AG-A025 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A026         TCGA-AG-A02G         TCGA-AG-A02X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A032 
"13Q LOSS WILD-TYPE" 
D61V2, multiclass
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 67 
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AG-3574 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3575         TCGA-AG-3578         TCGA-AG-3580 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3584         TCGA-AG-3586         TCGA-AG-3587 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3593         TCGA-AG-3598         TCGA-AG-3599 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3601         TCGA-AG-3602         TCGA-AG-3605 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3608         TCGA-AG-3609         TCGA-AG-3611 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3612         TCGA-AG-3726         TCGA-AG-3727 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3728         TCGA-AG-3878         TCGA-AG-3881 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3882         TCGA-AG-3883         TCGA-AG-3885 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3890         TCGA-AG-3892 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3898         TCGA-AG-3901         TCGA-AG-3902 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3909         TCGA-AG-3999         TCGA-AG-4001 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4005         TCGA-AG-4007         TCGA-AG-4008 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4015         TCGA-AG-A002         TCGA-AG-A008 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A00C         TCGA-AG-A00H         TCGA-AG-A00Y 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A011         TCGA-AG-A014         TCGA-AG-A015 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01J         TCGA-AG-A01L 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01N         TCGA-AG-A023         TCGA-AG-A025 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A026         TCGA-AG-A02G         TCGA-AG-A02X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A032 
"13Q LOSS WILD-TYPE" 
D61V3, multiclass
D61V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                 24
  CLUS_2                0                 38
  CLUS_3                1                 28
D61V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                3                 50
  CLUS_2                2                 31
  CLUS_3                0                 40
D61V6, multiclass
D61V7, multiclass
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 69 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-3913         TCGA-AG-3574         TCGA-AG-3575 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3598         TCGA-AG-3599         TCGA-AG-3601 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3602         TCGA-AG-3605         TCGA-AG-3608 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3609         TCGA-AG-3611         TCGA-AG-3612 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3726         TCGA-AG-3727         TCGA-AG-3728 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3878         TCGA-AG-3881         TCGA-AG-3882 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3885         TCGA-AG-3887 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3890         TCGA-AG-3892         TCGA-AG-3893 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3896         TCGA-AG-3898 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3901         TCGA-AG-3909         TCGA-AG-3999 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-A002 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D61V8, multiclass
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 69 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-3913         TCGA-AG-3574         TCGA-AG-3575 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3598         TCGA-AG-3599         TCGA-AG-3601 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3602         TCGA-AG-3605         TCGA-AG-3608 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3609         TCGA-AG-3611         TCGA-AG-3612 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3726         TCGA-AG-3727         TCGA-AG-3728 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3878         TCGA-AG-3881         TCGA-AG-3882 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3885         TCGA-AG-3887 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3890         TCGA-AG-3892         TCGA-AG-3893 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3896         TCGA-AG-3898 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3901         TCGA-AG-3909         TCGA-AG-3999 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-A002 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D61V9, multiclass
D61V10, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                2                 61
  CLUS_3                3                 56

Clustering(62) Variable = 14q loss mutation analysis
D62V1, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                7                 18
  CLUS_2                6                 14
  CLUS_3                9                 15
D62V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                9                 10
  CLUS_2                7                 17
  CLUS_3                6                 20
D62V3, multiclass
D62V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                9                 17
  CLUS_2               12                 26
  CLUS_3                9                 20
D62V5, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               20                 33
  CLUS_2               11                 22
  CLUS_3               10                 30
D62V6, multiclass
D62V7, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                8                  9
  CLUS_3                6                 10
  CLUS_4                3                 17
D62V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                5                 12
  CLUS_2                6                 18
  CLUS_3               10                 20
D62V9, multiclass
D62V10, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                6                 13
  CLUS_2               17                 46
  CLUS_3               23                 36

Clustering(63) Variable = 15q loss mutation analysis
D63V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                9                 16
  CLUS_2                8                 12
  CLUS_3               11                 13
D63V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               11                  8
  CLUS_2                8                 16
  CLUS_3                9                 17
D63V3, multiclass
D63V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                6                 20
  CLUS_2               14                 24
  CLUS_3               11                 18
D63V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1               25                 28
  CLUS_2                6                 27
  CLUS_3               16                 24
D63V6, multiclass
D63V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                8                 10
  CLUS_2                8                  9
  CLUS_3                6                 10
  CLUS_4                6                 14
D63V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                8                  9
  CLUS_2                9                 15
  CLUS_3               11                 19
D63V9, multiclass
D63V10, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                5                 14
  CLUS_2               22                 41
  CLUS_3               22                 37

Clustering(64) Variable = 16p loss mutation analysis
D64V1, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 25
  CLUS_2                2                 18
  CLUS_3                1                 23
D64V2, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                0                 24
  CLUS_3                2                 24
D64V3, multiclass
D64V4, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 26
  CLUS_2                1                 37
  CLUS_3                2                 27
D64V5, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                3                 50
  CLUS_2                2                 31
  CLUS_3                1                 39
D64V6, multiclass
D64V7, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                2                 15
  CLUS_3                0                 16
  CLUS_4                1                 19
D64V8, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 16
  CLUS_2                2                 22
  CLUS_3                0                 30
D64V9, multiclass
D64V10, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                3                 60
  CLUS_3                3                 56

Clustering(65) Variable = 16q loss mutation analysis
D65V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 25
  CLUS_2                4                 16
  CLUS_3                1                 23
D65V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 18
  CLUS_2                0                 24
  CLUS_3                4                 22
D65V3, multiclass
D65V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 26
  CLUS_2                3                 35
  CLUS_3                2                 27
D65V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                 48
  CLUS_2                2                 31
  CLUS_3                1                 39
D65V6, multiclass
D65V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                3                 14
  CLUS_3                0                 16
  CLUS_4                2                 18
D65V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 16
  CLUS_2                3                 21
  CLUS_3                1                 29
D65V9, multiclass
D65V10, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                5                 58
  CLUS_3                5                 54

Clustering(66) Variable = 17p loss mutation analysis
D66V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               13                 12
  CLUS_2               12                  8
  CLUS_3               14                 10
D66V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               11                  8
  CLUS_2               13                 11
  CLUS_3               15                 11
D66V3, multiclass
D66V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               14                 12
  CLUS_2               19                 19
  CLUS_3               18                 11
D66V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               31                 22
  CLUS_2               15                 18
  CLUS_3               26                 14
D66V6, multiclass
D66V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               12                  6
  CLUS_2               10                  7
  CLUS_3                9                  7
  CLUS_4                8                 12
D66V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               11                  6
  CLUS_2               12                 12
  CLUS_3               16                 14
D66V9, multiclass
D66V10, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               11                  8
  CLUS_2               33                 30
  CLUS_3               33                 26

Clustering(67) Variable = 17q loss mutation analysis
D67V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                 22
  CLUS_2                1                 19
  CLUS_3                1                 23
D67V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 19
  CLUS_2                3                 21
  CLUS_3                2                 24
D67V3, multiclass
D67V4, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 24
  CLUS_2                2                 36
  CLUS_3                6                 23
D67V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                6                 47
  CLUS_2                2                 31
  CLUS_3                5                 35
D67V6, multiclass
D67V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                 16
  CLUS_3                0                 16
  CLUS_4                2                 18
D67V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 16
  CLUS_2                2                 22
  CLUS_3                1                 29
D67V9, multiclass
D67V10, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                5                 58
  CLUS_3                7                 52

Clustering(68) Variable = 18p loss mutation analysis
D68V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               15                 10
  CLUS_2               12                  8
  CLUS_3               22                  2
D68V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               18                  1
  CLUS_2               16                  8
  CLUS_3               15                 11
D68V3, multiclass
D68V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               21                  5
  CLUS_2               26                 12
  CLUS_3               19                 10
D68V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               37                 16
  CLUS_2               20                 13
  CLUS_3               31                  9
D68V6, multiclass
D68V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               14                  4
  CLUS_2               13                  4
  CLUS_3               13                  3
  CLUS_4                9                 11
D68V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               12                  5
  CLUS_2               14                 10
  CLUS_3               23                  7
D68V9, multiclass
D68V10, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               12                  7
  CLUS_2               42                 21
  CLUS_3               45                 14

Clustering(69) Variable = 18q loss mutation analysis
D69V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               16                  9
  CLUS_2               15                  5
  CLUS_3               23                  1
D69V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               19                  0
  CLUS_2               17                  7
  CLUS_3               18                  8
D69V3, multiclass
D69V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               23                  3
  CLUS_2               28                 10
  CLUS_3               22                  7
D69V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               42                 11
  CLUS_2               24                  9
  CLUS_3               32                  8
D69V6, multiclass
D69V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               14                  4
  CLUS_2               16                  1
  CLUS_3               14                  2
  CLUS_4               11                  9
D69V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               13                  4
  CLUS_2               17                  7
  CLUS_3               25                  5
D69V9, multiclass
D69V10, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               15                  4
  CLUS_2               47                 16
  CLUS_3               48                 11

Clustering(70) Variable = 19p loss mutation analysis
D70V1, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 68 
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AG-3574 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3575         TCGA-AG-3578         TCGA-AG-3580 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3584         TCGA-AG-3586         TCGA-AG-3587 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3593         TCGA-AG-3594         TCGA-AG-3598 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3600         TCGA-AG-3601 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3602         TCGA-AG-3605         TCGA-AG-3608 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3609         TCGA-AG-3611         TCGA-AG-3612 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3726         TCGA-AG-3727         TCGA-AG-3728 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3878         TCGA-AG-3882         TCGA-AG-3883 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-3909         TCGA-AG-3999 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-A002 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A023 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A02X         TCGA-AG-A032 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D70V2, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 68 
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AG-3574 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3575         TCGA-AG-3578         TCGA-AG-3580 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3584         TCGA-AG-3586         TCGA-AG-3587 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3593         TCGA-AG-3594         TCGA-AG-3598 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3600         TCGA-AG-3601 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3602         TCGA-AG-3605         TCGA-AG-3608 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3609         TCGA-AG-3611         TCGA-AG-3612 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3726         TCGA-AG-3727         TCGA-AG-3728 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3878         TCGA-AG-3882         TCGA-AG-3883 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-3909         TCGA-AG-3999 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-A002 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A023 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A02X         TCGA-AG-A032 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D70V3, multiclass
D70V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                3                 23
  CLUS_2                1                 37
  CLUS_3                2                 27
D70V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                 49
  CLUS_2                1                 32
  CLUS_3                2                 38
D70V6, multiclass
D70V7, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 70 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-3913         TCGA-AG-3574         TCGA-AG-3575 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3609 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3611         TCGA-AG-3612         TCGA-AG-3726 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3878 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3882         TCGA-AG-3883         TCGA-AG-3885 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3890         TCGA-AG-3892 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3898         TCGA-AG-3901         TCGA-AG-3909 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4005 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4015 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A032 
"19P LOSS WILD-TYPE" 
D70V8, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 70 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-3913         TCGA-AG-3574         TCGA-AG-3575 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3609 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3611         TCGA-AG-3612         TCGA-AG-3726 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3878 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3882         TCGA-AG-3883         TCGA-AG-3885 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3890         TCGA-AG-3892 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3898         TCGA-AG-3901         TCGA-AG-3909 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4005 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4015 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A032 
"19P LOSS WILD-TYPE" 
D70V9, multiclass
D70V10, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                1                 62
  CLUS_3                4                 55

Clustering(71) Variable = 19q loss mutation analysis
D71V1, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 67 
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AG-3574 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3575         TCGA-AG-3578         TCGA-AG-3580 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3584         TCGA-AG-3586         TCGA-AG-3587 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3593         TCGA-AG-3594         TCGA-AG-3598 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3600         TCGA-AG-3601 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3602         TCGA-AG-3605         TCGA-AG-3608 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3609         TCGA-AG-3611         TCGA-AG-3612 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3726         TCGA-AG-3727         TCGA-AG-3728 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3878         TCGA-AG-3882         TCGA-AG-3883 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-3909         TCGA-AG-3999 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-A002 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A014         TCGA-AG-A015 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01J         TCGA-AG-A01L 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01N         TCGA-AG-A023         TCGA-AG-A025 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A026         TCGA-AG-A02G         TCGA-AG-A02X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A032 
"19Q LOSS WILD-TYPE" 
D71V2, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 67 
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AG-3574 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3575         TCGA-AG-3578         TCGA-AG-3580 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3584         TCGA-AG-3586         TCGA-AG-3587 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3593         TCGA-AG-3594         TCGA-AG-3598 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3600         TCGA-AG-3601 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3602         TCGA-AG-3605         TCGA-AG-3608 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3609         TCGA-AG-3611         TCGA-AG-3612 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3726         TCGA-AG-3727         TCGA-AG-3728 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3878         TCGA-AG-3882         TCGA-AG-3883 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-3909         TCGA-AG-3999 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-A002 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A014         TCGA-AG-A015 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01J         TCGA-AG-A01L 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01N         TCGA-AG-A023         TCGA-AG-A025 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A026         TCGA-AG-A02G         TCGA-AG-A02X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A032 
"19Q LOSS WILD-TYPE" 
D71V3, multiclass
D71V4, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                 24
  CLUS_2                0                 38
  CLUS_3                3                 26
D71V5, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                 51
  CLUS_2                1                 32
  CLUS_3                3                 37
D71V6, multiclass
D71V7, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 69 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-3913         TCGA-AG-3574         TCGA-AG-3575 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3609 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3611         TCGA-AG-3612         TCGA-AG-3726 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3878 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3882         TCGA-AG-3883         TCGA-AG-3885 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3890         TCGA-AG-3892 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3898         TCGA-AG-3901         TCGA-AG-3909 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4005 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4015 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A014 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D71V8, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 69 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-3913         TCGA-AG-3574         TCGA-AG-3575 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3609 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3611         TCGA-AG-3612         TCGA-AG-3726 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3878 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3882         TCGA-AG-3883         TCGA-AG-3885 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3890         TCGA-AG-3892 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3898         TCGA-AG-3901         TCGA-AG-3909 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4005 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4015 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A014 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D71V9, multiclass
D71V10, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                 17
  CLUS_2                2                 61
  CLUS_3                2                 57

Clustering(72) Variable = 20p loss mutation analysis
D72V1, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                4                 21
  CLUS_2                3                 17
  CLUS_3                4                 20
D72V2, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                3                 16
  CLUS_2                4                 20
  CLUS_3                4                 22
D72V3, multiclass
D72V4, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                3                 23
  CLUS_2                2                 36
  CLUS_3                3                 26
D72V5, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                4                 49
  CLUS_2                4                 29
  CLUS_3                8                 32
D72V6, multiclass
D72V7, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                 16
  CLUS_3                5                 11
  CLUS_4                3                 17
D72V8, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                 15
  CLUS_2                4                 20
  CLUS_3                6                 24
D72V9, multiclass
D72V10, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                 17
  CLUS_2               11                 52
  CLUS_3                3                 56

Clustering(73) Variable = 21q loss mutation analysis
D73V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                5                 20
  CLUS_2                5                 15
  CLUS_3                6                 18
D73V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                5                 14
  CLUS_2                4                 20
  CLUS_3                7                 19
D73V3, multiclass
D73V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                9                 17
  CLUS_2                9                 29
  CLUS_3                9                 20
D73V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               19                 34
  CLUS_2                6                 27
  CLUS_3                9                 31
D73V6, multiclass
D73V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                4                 13
  CLUS_3                5                 11
  CLUS_4                5                 15
D73V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                 13
  CLUS_2                7                 17
  CLUS_3                7                 23
D73V9, multiclass
D73V10, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                7                 12
  CLUS_2               17                 46
  CLUS_3               16                 43

Clustering(74) Variable = 22q loss mutation analysis
D74V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                6                 19
  CLUS_2                6                 14
  CLUS_3                6                 18
D74V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                5                 14
  CLUS_2                5                 19
  CLUS_3                8                 18
D74V3, multiclass
D74V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                4                 22
  CLUS_2               12                 26
  CLUS_3                9                 20
D74V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               16                 37
  CLUS_2                7                 26
  CLUS_3               10                 30
D74V6, multiclass
D74V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                7                 11
  CLUS_2                4                 13
  CLUS_3                4                 12
  CLUS_4                4                 16
D74V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                4                 13
  CLUS_2                7                 17
  CLUS_3                8                 22
D74V9, multiclass
D74V10, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                4                 15
  CLUS_2               18                 45
  CLUS_3               18                 41

Clustering(75) Variable = Xq loss mutation analysis
D75V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2                23
  CLUS_2               0                20
  CLUS_3               1                23
D75V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               2                22
  CLUS_3               0                26
D75V3, multiclass
D75V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                26
  CLUS_2               1                37
  CLUS_3               2                27
D75V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               3                50
  CLUS_2               1                32
  CLUS_3               1                39
D75V6, multiclass
D75V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               0                17
  CLUS_3               1                15
  CLUS_4               1                19
D75V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                16
  CLUS_2               1                23
  CLUS_3               1                29
D75V9, multiclass
D75V10, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                18
  CLUS_2               2                61
  CLUS_3               2                57
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"               "CN_CNMF" 
                     V4                      V5                      V6 
     "METHLYATION_CNMF"             "RPPA_CNMF"    "RPPA_CHIERARCHICAL" 
                     V7                      V8                      V9 
         "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF" 
                    V10 
 "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
