
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/376042/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/BLCA-TP/2909272/1.GDAC_mergedClustering.Finished/BLCA-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=BLCA-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=BLCA-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=153, in cluster file=150, common to both=150
[1] "Reduce the number of clustering variables from 80 to 76."
[1]  76 150
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               16               134 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               16               134 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32               118 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32               118 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               28               122 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               28               122 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               11               139 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               11               139 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               30               120 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               30               120 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               42               108 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               42               108 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               142 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               142 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               147 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               147 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               40               110 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               40               110 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               18               132 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               18               132 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                8               142 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                8               142 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5               145 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5               145 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               46               104 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               46               104 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               43               107 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               43               107 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               15               135 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               15               135 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               39               111 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               39               111 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               15               135 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               15               135 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11               139 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11               139 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                28                122 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                28                122 
[1] "10q gain mutation analysis"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                143 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                143 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                142 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                142 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                142 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                142 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                24                126 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                24                126 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                17                133 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                17                133 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                25                125 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                25                125 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                139 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                139 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                145 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                145 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                10                140 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                10                140 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                137 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                13                137 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 9                141 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 9                141 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                25                125 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                25                125 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                26                124 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                26                124 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                141 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                141 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                15                135 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                15                135 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                29                121 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                29                121 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                54                 96 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                54                 96 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                59                 91 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                59                 91 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                27                123 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                27                123 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                12                138 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                12                138 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6               144 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6               144 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4               146 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4               146 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                8               142 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                8               142 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               17               133 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               17               133 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9               141 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9               141 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               29               121 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               29               121 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               26               124 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               26               124 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               14               136 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               14               136 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               36               114 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               36               114 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               18               132 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               18               132 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               29               121 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               29               121 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               147 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               147 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               49               101 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               49               101 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5               145 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5               145 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               43               107 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               43               107 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               41               109 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               41               109 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                19                131 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                19                131 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                30                120 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                30                120 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                48                102 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                48                102 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                35                115 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                35                115 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                144 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                144 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 9                141 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 9                141 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                130 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                130 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                25                125 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                25                125 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                19                131 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                19                131 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                17                133 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                17                133 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                17                133 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                17                133 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                42                108 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                42                108 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                144 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                144 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                22                128 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                22                128 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                39                111 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                39                111 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 9                141 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 9                141 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                146 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                146 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                143 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                143 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                17                133 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                17                133 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                29                121 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                29                121 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4               146 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4               146 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "RPPA_CNMF"            
[4] "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 8 rows and 150 columns.

Variable 1:'CN_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "RPPA_CNMF"            
[4] "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 150 columns, 0 survival variables, and 8 non-survival variables.
CN_CNMF, nv=6, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, multiclass
D1V2, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               7                29
  CLUS_2               6                44
  CLUS_3               2                37
  CLUS_4               1                24
D1V3, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               0                10
  CLUS_3               1                13
  CLUS_4               3                13
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                11
  CLUS_2               2                12
  CLUS_3               2                22
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               4                46
  CLUS_2               4                29
  CLUS_3               6                32
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               6                33
  CLUS_2               3                15
  CLUS_3               5                59
D1V7, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3                32
  CLUS_2              10                58
  CLUS_3               2                44
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                 6
  CLUS_2               2                30
  CLUS_3              11                98

Clustering(2) Variable = 1q gain mutation analysis
D2V1, multiclass
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              10                26
  CLUS_2               8                42
  CLUS_3              10                29
  CLUS_4               4                21
D2V3, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               3                 7
  CLUS_3               3                11
  CLUS_4               4                12
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3                10
  CLUS_2               2                12
  CLUS_3               7                17
D2V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              12                38
  CLUS_2               8                25
  CLUS_3               7                31
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               7                32
  CLUS_2               5                13
  CLUS_3              15                49
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               5                30
  CLUS_2              17                51
  CLUS_3               9                37
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                 6
  CLUS_2               5                27
  CLUS_3              24                85

Clustering(3) Variable = 2p gain mutation analysis
D3V1, multiclass
D3V2, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              15                21
  CLUS_2               7                43
  CLUS_3               5                34
  CLUS_4               1                24
D3V3, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                10
  CLUS_2               1                 9
  CLUS_3               6                 8
  CLUS_4               4                12
D3V4, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               3                10
  CLUS_2               2                12
  CLUS_3               7                17
D3V5, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              13                37
  CLUS_2               4                29
  CLUS_3               7                31
D3V6, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               6                33
  CLUS_2               4                14
  CLUS_3              14                50
D3V7, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1              11                24
  CLUS_2              11                57
  CLUS_3               5                41
D3V8, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               0                 8
  CLUS_2              10                22
  CLUS_3              17                92

Clustering(4) Variable = 2q gain mutation analysis
D4V1, multiclass
D4V2, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               5                31
  CLUS_2               3                47
  CLUS_3               3                36
  CLUS_4               0                25
D4V3, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                11
  CLUS_2               0                10
  CLUS_3               1                13
  CLUS_4               2                14
D4V4, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               0                14
  CLUS_3               2                22
D4V5, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               6                44
  CLUS_2               1                32
  CLUS_3               2                36
D4V6, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                38
  CLUS_2               2                16
  CLUS_3               6                58
D4V7, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               5                30
  CLUS_2               3                65
  CLUS_3               3                43
D4V8, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               5                27
  CLUS_3               6               103

Clustering(5) Variable = 3p gain mutation analysis
D5V1, multiclass
D5V2, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               8                28
  CLUS_2               4                46
  CLUS_3              11                28
  CLUS_4               7                18
D5V3, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                11
  CLUS_2               4                 6
  CLUS_3               4                10
  CLUS_4               1                15
D5V4, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               0                14
  CLUS_3               8                16
D5V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              15                35
  CLUS_2               7                26
  CLUS_3               4                34
D5V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                36
  CLUS_2               2                16
  CLUS_3              21                43
D5V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              12                23
  CLUS_2               8                60
  CLUS_3              10                36
D5V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                 7
  CLUS_2              11                21
  CLUS_3              18                91

Clustering(6) Variable = 3q gain mutation analysis
D6V1, multiclass
D6V2, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              12                24
  CLUS_2               9                41
  CLUS_3              13                26
  CLUS_4               8                17
D6V3, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                 8
  CLUS_2               3                 7
  CLUS_3               4                10
  CLUS_4               4                12
D6V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2                11
  CLUS_2               2                12
  CLUS_3              10                14
D6V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              17                33
  CLUS_2               9                24
  CLUS_3               9                29
D6V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               7                32
  CLUS_2               4                14
  CLUS_3              24                40
D6V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              14                21
  CLUS_2              17                51
  CLUS_3              11                35
D6V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                 5
  CLUS_2              13                19
  CLUS_3              26                83

Clustering(7) Variable = 4p gain mutation analysis
D7V1, multiclass
D7V2, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3                33
  CLUS_2               3                47
  CLUS_3               2                37
  CLUS_4               0                25
D7V3, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                10
  CLUS_2               1                 9
  CLUS_3               2                12
  CLUS_4               2                14
D7V4, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                12
  CLUS_3               3                21
D7V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3                47
  CLUS_2               2                31
  CLUS_3               3                35
D7V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4                35
  CLUS_2               1                17
  CLUS_3               3                61
D7V7, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                33
  CLUS_2               5                63
  CLUS_3               1                45
D7V8, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               2                30
  CLUS_3               5               104

Clustering(8) Variable = 4q gain mutation analysis
D8V1, multiclass
D8V2, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2                34
  CLUS_2               1                49
  CLUS_3               0                39
  CLUS_4               0                25
D8V3, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                50 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C        TCGA-CU-A0YN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6        TCGA-DK-A1AA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD        TCGA-DK-A1AE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-H4-A2HQ        TCGA-HQ-A2OE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V4, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                50 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C        TCGA-CU-A0YN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6        TCGA-DK-A1AA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD        TCGA-DK-A1AE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-H4-A2HQ        TCGA-HQ-A2OE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2                48
  CLUS_2               0                33
  CLUS_3               1                37
D8V6, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2                37
  CLUS_2               0                18
  CLUS_3               1                63
D8V7, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                35
  CLUS_2               3                65
  CLUS_3               0                46
D8V8, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               0                32
  CLUS_3               2               107

Clustering(9) Variable = 5p gain mutation analysis
D9V1, multiclass
D9V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               8                28
  CLUS_2              15                35
  CLUS_3              13                26
  CLUS_4               4                21
D9V3, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               5                 6
  CLUS_2               2                 8
  CLUS_3               0                14
  CLUS_4               5                11
D9V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                10
  CLUS_2               5                 9
  CLUS_3               4                20
D9V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              14                36
  CLUS_2               7                26
  CLUS_3              14                24
D9V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              13                26
  CLUS_2               6                12
  CLUS_3              16                48
D9V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              13                22
  CLUS_2              18                50
  CLUS_3               9                37
D9V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                 6
  CLUS_2              12                20
  CLUS_3              26                83

Clustering(10) Variable = 5q gain mutation analysis
D10V1, multiclass
D10V2, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                34
  CLUS_2               6                44
  CLUS_3               9                30
  CLUS_4               1                24
D10V3, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                10
  CLUS_2               0                10
  CLUS_3               0                14
  CLUS_4               3                13
D10V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                11
  CLUS_2               0                14
  CLUS_3               2                22
D10V5, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               8                42
  CLUS_2               3                30
  CLUS_3               5                33
D10V6, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               5                34
  CLUS_2               2                16
  CLUS_3               9                55
D10V7, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               6                29
  CLUS_2              10                58
  CLUS_3               2                44
D10V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               6                26
  CLUS_3              12                97

Clustering(11) Variable = 6p gain mutation analysis
D11V1, multiclass
D11V2, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               3                33
  CLUS_2               1                49
  CLUS_3               4                35
  CLUS_4               0                25
D11V3, multiclass
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2                49 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AD        TCGA-DK-A1AE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HQ-A2OE 
"6P GAIN WILD-TYPE" 
D11V4, multiclass
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2                49 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AD        TCGA-DK-A1AE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HQ-A2OE 
"6P GAIN WILD-TYPE" 
D11V5, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                48
  CLUS_2               1                32
  CLUS_3               2                36
D11V6, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               3                36
  CLUS_2               1                17
  CLUS_3               1                63
D11V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               3                32
  CLUS_2               4                64
  CLUS_3               1                45
D11V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               3                29
  CLUS_3               4               105

Clustering(12) Variable = 6q gain mutation analysis
D12V1, multiclass
D12V2, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               3                33
  CLUS_2               1                49
  CLUS_3               1                38
  CLUS_4               0                25
D12V3, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                49 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0        TCGA-C4-A0F6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C        TCGA-CU-A0YN 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6        TCGA-DK-A1AA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A1AB        TCGA-DK-A1AD        TCGA-DK-A1AE        TCGA-DK-A1AF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1        TCGA-DK-A2I2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4        TCGA-G2-A2EF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL        TCGA-G2-A2EO 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HQ-A2OE 
"6Q GAIN WILD-TYPE" 
D12V4, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                49 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0        TCGA-C4-A0F6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C        TCGA-CU-A0YN 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6        TCGA-DK-A1AA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A1AB        TCGA-DK-A1AD        TCGA-DK-A1AE        TCGA-DK-A1AF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1        TCGA-DK-A2I2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4        TCGA-G2-A2EF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL        TCGA-G2-A2EO 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HQ-A2OE 
"6Q GAIN WILD-TYPE" 
D12V5, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2               119 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BL-A3JM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A0S7        TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A20O        TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A20T        TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A20X        TCGA-BT-A2LB        TCGA-BT-A2LD        TCGA-BT-A3PH 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A3PJ        TCGA-BT-A3PK        TCGA-C4-A0F0        TCGA-C4-A0F6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C        TCGA-CF-A3MF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CF-A3MG        TCGA-CF-A3MH        TCGA-CF-A3MI        TCGA-CU-A0YN 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CU-A0YO        TCGA-CU-A0YR        TCGA-CU-A3KJ        TCGA-CU-A3QU 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CU-A3YL        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A1A7        TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AD 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A1AE        TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A2I1        TCGA-DK-A2I2        TCGA-DK-A2I4        TCGA-DK-A2I6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A3IK        TCGA-DK-A3IL        TCGA-DK-A3IM        TCGA-DK-A3IN 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A3IS        TCGA-DK-A3IT        TCGA-DK-A3IU        TCGA-DK-A3IV 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A3WX        TCGA-DK-A3WY        TCGA-DK-A3X1        TCGA-DK-A3X2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-E5-A2PC        TCGA-E7-A3X6        TCGA-E7-A3Y1        TCGA-FD-A3B3 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FD-A3B4        TCGA-FD-A3B5        TCGA-FD-A3B6        TCGA-FD-A3B7 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FD-A3B8        TCGA-FD-A3N5        TCGA-FD-A3N6        TCGA-FD-A3NA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FD-A3SJ        TCGA-FD-A3SL        TCGA-FD-A3SM        TCGA-FD-A3SN 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FD-A3SO        TCGA-FD-A3SP        TCGA-FD-A3SQ        TCGA-FD-A3SR 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FD-A3SS        TCGA-FT-A3EE        TCGA-G2-A2EF        TCGA-G2-A2EJ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G2-A2EK        TCGA-G2-A2EL        TCGA-G2-A2EO        TCGA-G2-A2ES 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G2-A3IB        TCGA-G2-A3IE        TCGA-G2-A3VY        TCGA-GC-A3BM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GC-A3I6        TCGA-GC-A3OO        TCGA-GC-A3RB        TCGA-GC-A3RC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GC-A3RD        TCGA-GC-A3WC        TCGA-GD-A2C5        TCGA-GD-A3OP 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GD-A3OQ        TCGA-GD-A3OS        TCGA-GV-A3JV        TCGA-GV-A3JW 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GV-A3JX        TCGA-GV-A3JZ        TCGA-GV-A3QF        TCGA-GV-A3QG 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GV-A3QH        TCGA-GV-A3QI        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HQ-A2OE        TCGA-K4-A3WS        TCGA-K4-A3WV 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D12V6, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2               119 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BL-A3JM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A0S7        TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A20O        TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A20T        TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A20X        TCGA-BT-A2LB        TCGA-BT-A2LD        TCGA-BT-A3PH 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A3PJ        TCGA-BT-A3PK        TCGA-C4-A0F0        TCGA-C4-A0F6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C        TCGA-CF-A3MF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CF-A3MG        TCGA-CF-A3MH        TCGA-CF-A3MI        TCGA-CU-A0YN 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CU-A0YO        TCGA-CU-A0YR        TCGA-CU-A3KJ        TCGA-CU-A3QU 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CU-A3YL        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A1A7        TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AD 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A1AE        TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A2I1        TCGA-DK-A2I2        TCGA-DK-A2I4        TCGA-DK-A2I6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A3IK        TCGA-DK-A3IL        TCGA-DK-A3IM        TCGA-DK-A3IN 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A3IS        TCGA-DK-A3IT        TCGA-DK-A3IU        TCGA-DK-A3IV 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A3WX        TCGA-DK-A3WY        TCGA-DK-A3X1        TCGA-DK-A3X2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-E5-A2PC        TCGA-E7-A3X6        TCGA-E7-A3Y1        TCGA-FD-A3B3 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FD-A3B4        TCGA-FD-A3B5        TCGA-FD-A3B6        TCGA-FD-A3B7 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FD-A3B8        TCGA-FD-A3N5        TCGA-FD-A3N6        TCGA-FD-A3NA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FD-A3SJ        TCGA-FD-A3SL        TCGA-FD-A3SM        TCGA-FD-A3SN 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FD-A3SO        TCGA-FD-A3SP        TCGA-FD-A3SQ        TCGA-FD-A3SR 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FD-A3SS        TCGA-FT-A3EE        TCGA-G2-A2EF        TCGA-G2-A2EJ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G2-A2EK        TCGA-G2-A2EL        TCGA-G2-A2EO        TCGA-G2-A2ES 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G2-A3IB        TCGA-G2-A3IE        TCGA-G2-A3VY        TCGA-GC-A3BM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GC-A3I6        TCGA-GC-A3OO        TCGA-GC-A3RB        TCGA-GC-A3RC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GC-A3RD        TCGA-GC-A3WC        TCGA-GD-A2C5        TCGA-GD-A3OP 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GD-A3OQ        TCGA-GD-A3OS        TCGA-GV-A3JV        TCGA-GV-A3JW 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GV-A3JX        TCGA-GV-A3JZ        TCGA-GV-A3QF        TCGA-GV-A3QG 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GV-A3QH        TCGA-GV-A3QI        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HQ-A2OE        TCGA-K4-A3WS        TCGA-K4-A3WV 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D12V7, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               3                32
  CLUS_2               2                66
  CLUS_3               0                46
D12V8, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               3                29
  CLUS_3               2               107

Clustering(13) Variable = 7p gain mutation analysis
D13V1, multiclass
D13V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              19                17
  CLUS_2              13                37
  CLUS_3              12                27
  CLUS_4               2                23
D13V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               3                 8
  CLUS_2               2                 8
  CLUS_3               5                 9
  CLUS_4               6                10
D13V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4                 9
  CLUS_2               2                12
  CLUS_3              10                14
D13V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              16                34
  CLUS_2              10                23
  CLUS_3              11                27
D13V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              12                27
  CLUS_2               6                12
  CLUS_3              19                45
D13V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              14                21
  CLUS_2              25                43
  CLUS_3               7                39
D13V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4                 4
  CLUS_2              12                20
  CLUS_3              30                79

Clustering(14) Variable = 7q gain mutation analysis
D14V1, multiclass
D14V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              16                20
  CLUS_2              13                37
  CLUS_3              11                28
  CLUS_4               3                22
D14V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                 7
  CLUS_2               3                 7
  CLUS_3               5                 9
  CLUS_4               5                11
D14V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                10
  CLUS_2               3                11
  CLUS_3              11                13
D14V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              15                35
  CLUS_2               9                24
  CLUS_3              12                26
D14V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              12                27
  CLUS_2               6                12
  CLUS_3              18                46
D14V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              12                23
  CLUS_2              21                47
  CLUS_3              10                36
D14V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                 4
  CLUS_2              10                22
  CLUS_3              29                80

Clustering(15) Variable = 8p gain mutation analysis
D15V1, multiclass
D15V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                34
  CLUS_2               3                47
  CLUS_3              10                29
  CLUS_4               0                25
D15V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                11
  CLUS_2               1                 9
  CLUS_3               2                12
  CLUS_4               5                11
D15V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               4                 9
  CLUS_2               1                13
  CLUS_3               3                21
D15V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               6                44
  CLUS_2               1                32
  CLUS_3               8                30
D15V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               5                34
  CLUS_2               2                16
  CLUS_3               8                56
D15V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3                32
  CLUS_2               9                59
  CLUS_3               3                43
D15V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               3                29
  CLUS_3              12                97

Clustering(16) Variable = 8q gain mutation analysis
D16V1, multiclass
D16V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              13                23
  CLUS_2              10                40
  CLUS_3              13                26
  CLUS_4               3                22
D16V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               3                 8
  CLUS_2               3                 7
  CLUS_3               3                11
  CLUS_4               7                 9
D16V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               6                 7
  CLUS_2               4                10
  CLUS_3               6                18
D16V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              17                33
  CLUS_2               6                27
  CLUS_3              12                26
D16V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              10                29
  CLUS_2               5                13
  CLUS_3              20                44
D16V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               8                27
  CLUS_2              21                47
  CLUS_3              10                36
D16V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                 6
  CLUS_2               7                25
  CLUS_3              30                79

Clustering(17) Variable = 9p gain mutation analysis
D17V1, multiclass
D17V2, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               6                30
  CLUS_2               4                46
  CLUS_3               4                35
  CLUS_4               1                24
D17V3, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3                 8
  CLUS_2               1                 9
  CLUS_3               0                14
  CLUS_4               2                14
D17V4, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                12
  CLUS_3               3                21
D17V5, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4                46
  CLUS_2               4                29
  CLUS_3               6                32
D17V6, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               6                33
  CLUS_2               4                14
  CLUS_3               4                60
D17V7, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               3                32
  CLUS_2              11                57
  CLUS_3               1                45
D17V8, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               3                29
  CLUS_3              11                98

Clustering(18) Variable = 9q gain mutation analysis
D18V1, multiclass
D18V2, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4                32
  CLUS_2               5                45
  CLUS_3               2                37
  CLUS_4               0                25
D18V3, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4                 7
  CLUS_2               0                10
  CLUS_3               1                13
  CLUS_4               2                14
D18V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                12
  CLUS_2               3                11
  CLUS_3               3                21
D18V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                49
  CLUS_2               5                28
  CLUS_3               5                33
D18V6, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               6                33
  CLUS_2               3                15
  CLUS_3               2                62
D18V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3                32
  CLUS_2               6                62
  CLUS_3               2                44
D18V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               2                30
  CLUS_3               8               101

Clustering(19) Variable = 10p gain mutation analysis
D19V1, multiclass
D19V2, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               13                 23
  CLUS_2                7                 43
  CLUS_3                8                 31
  CLUS_4                0                 25
D19V3, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                4                  6
  CLUS_3                3                 11
  CLUS_4                5                 11
D19V4, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                4                  9
  CLUS_2                0                 14
  CLUS_3                9                 15
D19V5, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               13                 37
  CLUS_2                7                 26
  CLUS_3                6                 32
D19V6, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                7                 32
  CLUS_2                3                 15
  CLUS_3               16                 48
D19V7, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                9                 26
  CLUS_2               10                 58
  CLUS_3                9                 37
D19V8, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                0                  8
  CLUS_2                9                 23
  CLUS_3               19                 90

Clustering(20) Variable = 10q gain mutation analysis
D20V1, multiclass
D20V2, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                4                 32
  CLUS_2                1                 49
  CLUS_3                2                 37
  CLUS_4                0                 25
D20V3, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                2                  8
  CLUS_3                1                 13
  CLUS_4                2                 14
D20V4, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                0                 14
  CLUS_3                4                 20
D20V5, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                4                 46
  CLUS_2                2                 31
  CLUS_3                1                 37
D20V6, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                 39
  CLUS_2                1                 17
  CLUS_3                6                 58
D20V7, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                 33
  CLUS_2                2                 66
  CLUS_3                3                 43
D20V8, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                  8
  CLUS_2                2                 30
  CLUS_3                5                104

Clustering(21) Variable = 11p gain mutation analysis
D21V1, multiclass
D21V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 34
  CLUS_2                2                 48
  CLUS_3                3                 36
  CLUS_4                1                 24
D21V3, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 50 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BT-A0S7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A0YX         TCGA-BT-A20J         TCGA-BT-A20N 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A20O         TCGA-BT-A20P         TCGA-BT-A20Q 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A20R         TCGA-BT-A20T         TCGA-BT-A20U 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A20V         TCGA-BT-A20W         TCGA-BT-A20X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A2LA         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2HX         TCGA-DK-A2I1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A2I2         TCGA-E5-A2PC         TCGA-FD-A3B3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FD-A3B4         TCGA-G2-A2EF         TCGA-G2-A2EJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G2-A2EK         TCGA-G2-A2EL         TCGA-G2-A2EO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G2-A2ES         TCGA-GD-A2C5         TCGA-H4-A2HO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-H4-A2HQ         TCGA-HQ-A2OE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D21V4, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 50 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BT-A0S7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A0YX         TCGA-BT-A20J         TCGA-BT-A20N 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A20O         TCGA-BT-A20P         TCGA-BT-A20Q 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A20R         TCGA-BT-A20T         TCGA-BT-A20U 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A20V         TCGA-BT-A20W         TCGA-BT-A20X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A2LA         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2HX         TCGA-DK-A2I1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A2I2         TCGA-E5-A2PC         TCGA-FD-A3B3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FD-A3B4         TCGA-G2-A2EF         TCGA-G2-A2EJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G2-A2EK         TCGA-G2-A2EL         TCGA-G2-A2EO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G2-A2ES         TCGA-GD-A2C5         TCGA-H4-A2HO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-H4-A2HQ         TCGA-HQ-A2OE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D21V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                4                 46
  CLUS_2                1                 32
  CLUS_3                3                 35
D21V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                 36
  CLUS_2                1                 17
  CLUS_3                4                 60
D21V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 34
  CLUS_2                6                 62
  CLUS_3                1                 45
D21V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                  7
  CLUS_2                1                 31
  CLUS_3                6                103

Clustering(22) Variable = 11q gain mutation analysis
D22V1, multiclass
D22V2, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                 33
  CLUS_2                2                 48
  CLUS_3                3                 36
  CLUS_4                0                 25
D22V3, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BT-A0S7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A0YX         TCGA-BT-A20J         TCGA-BT-A20N 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A20O         TCGA-BT-A20P         TCGA-BT-A20Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A20R         TCGA-BT-A20T         TCGA-BT-A20U 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A20V         TCGA-BT-A20W         TCGA-BT-A20X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A2LA         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DK-A1A5         TCGA-DK-A1A6         TCGA-DK-A1AA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DK-A1AB         TCGA-DK-A1AC         TCGA-DK-A1AD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HQ-A2OE 
"11Q GAIN WILD-TYPE" 
D22V4, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BT-A0S7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A0YX         TCGA-BT-A20J         TCGA-BT-A20N 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A20O         TCGA-BT-A20P         TCGA-BT-A20Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A20R         TCGA-BT-A20T         TCGA-BT-A20U 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A20V         TCGA-BT-A20W         TCGA-BT-A20X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A2LA         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DK-A1A5         TCGA-DK-A1A6         TCGA-DK-A1AA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DK-A1AB         TCGA-DK-A1AC         TCGA-DK-A1AD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HQ-A2OE 
"11Q GAIN WILD-TYPE" 
D22V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                 47
  CLUS_2                1                 32
  CLUS_3                4                 34
D22V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                 35
  CLUS_2                0                 18
  CLUS_3                4                 60
D22V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                 33
  CLUS_2                5                 63
  CLUS_3                1                 45
D22V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                  7
  CLUS_2                2                 30
  CLUS_3                5                104

Clustering(23) Variable = 12p gain mutation analysis
D23V1, multiclass
D23V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                7                 29
  CLUS_2                6                 44
  CLUS_3                8                 31
  CLUS_4                3                 22
D23V3, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                0                 10
  CLUS_3                1                 13
  CLUS_4                5                 11
D23V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                0                 14
  CLUS_3                4                 20
D23V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               10                 40
  CLUS_2                5                 28
  CLUS_3                7                 31
D23V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                6                 33
  CLUS_2                5                 13
  CLUS_3               11                 53
D23V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                6                 29
  CLUS_2               14                 54
  CLUS_3                4                 42
D23V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                  6
  CLUS_2                5                 27
  CLUS_3               17                 92

Clustering(24) Variable = 12q gain mutation analysis
D24V1, multiclass
D24V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                5                 31
  CLUS_2                3                 47
  CLUS_3                7                 32
  CLUS_4                2                 23
D24V3, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                0                 10
  CLUS_3                2                 12
  CLUS_4                4                 12
D24V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                1                 13
  CLUS_3                5                 19
D24V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                9                 41
  CLUS_2                4                 29
  CLUS_3                3                 35
D24V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                4                 35
  CLUS_2                3                 15
  CLUS_3                9                 55
D24V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                7                 28
  CLUS_2                9                 59
  CLUS_3                1                 45
D24V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                  7
  CLUS_2                6                 26
  CLUS_3               10                 99

Clustering(25) Variable = 13q gain mutation analysis
D25V1, multiclass
D25V2, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                7                 29
  CLUS_2                9                 41
  CLUS_3                6                 33
  CLUS_4                3                 22
D25V3, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                5                  6
  CLUS_2                1                  9
  CLUS_3                1                 13
  CLUS_4                1                 15
D25V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                5                  9
  CLUS_3                2                 22
D25V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                8                 42
  CLUS_2               11                 22
  CLUS_3                4                 34
D25V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                4                 35
  CLUS_2                7                 11
  CLUS_3               12                 52
D25V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                4                 31
  CLUS_2                9                 59
  CLUS_3               11                 35
D25V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                  8
  CLUS_2                5                 27
  CLUS_3               19                 90

Clustering(26) Variable = 14q gain mutation analysis
D26V1, multiclass
D26V2, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                 34
  CLUS_2                5                 45
  CLUS_3                3                 36
  CLUS_4                1                 24
D26V3, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                3                  8
  CLUS_2                0                 10
  CLUS_3                1                 13
  CLUS_4                1                 15
D26V4, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                2                 12
  CLUS_3                3                 21
D26V5, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                 48
  CLUS_2                2                 31
  CLUS_3                5                 33
D26V6, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                3                 36
  CLUS_2                3                 15
  CLUS_3                3                 61
D26V7, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                 33
  CLUS_2                6                 62
  CLUS_3                2                 44
D26V8, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                  8
  CLUS_2                1                 31
  CLUS_3                9                100

Clustering(27) Variable = 15q gain mutation analysis
D27V1, multiclass
D27V2, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                 36
  CLUS_2                0                 50
  CLUS_3                3                 36
  CLUS_4                2                 23
D27V3, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                1                  9
  CLUS_3                2                 12
  CLUS_4                0                 16
D27V4, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                0                 14
  CLUS_3                3                 21
D27V5, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                 49
  CLUS_2                2                 31
  CLUS_3                1                 37
D27V6, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                 38
  CLUS_2                0                 18
  CLUS_3                3                 61
D27V7, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                 34
  CLUS_2                2                 66
  CLUS_3                2                 44
D27V8, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                  8
  CLUS_2                1                 31
  CLUS_3                4                105

Clustering(28) Variable = 16p gain mutation analysis
D28V1, multiclass
D28V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                4                 32
  CLUS_2                2                 48
  CLUS_3                3                 36
  CLUS_4                1                 24
D28V3, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                1                  9
  CLUS_3                0                 14
  CLUS_4                2                 14
D28V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                 13
  CLUS_3                2                 22
D28V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                5                 45
  CLUS_2                2                 31
  CLUS_3                2                 36
D28V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                 36
  CLUS_2                2                 16
  CLUS_3                4                 60
D28V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 33
  CLUS_2                3                 65
  CLUS_3                4                 42
D28V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                  8
  CLUS_2                2                 30
  CLUS_3                7                102

Clustering(29) Variable = 16q gain mutation analysis
D29V1, multiclass
D29V2, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                5                 31
  CLUS_2                5                 45
  CLUS_3                3                 36
  CLUS_4                0                 25
D29V3, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                1                  9
  CLUS_3                1                 13
  CLUS_4                2                 14
D29V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                 13
  CLUS_3                3                 21
D29V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                5                 45
  CLUS_2                3                 30
  CLUS_3                4                 34
D29V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                5                 34
  CLUS_2                3                 15
  CLUS_3                4                 60
D29V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 33
  CLUS_2                5                 63
  CLUS_3                5                 41
D29V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                  7
  CLUS_2                2                 30
  CLUS_3                9                100

Clustering(30) Variable = 17p gain mutation analysis
D30V1, multiclass
D30V2, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                 33
  CLUS_2                3                 47
  CLUS_3                3                 36
  CLUS_4                0                 25
D30V3, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 49 
        TCGA-BL-A13I         TCGA-BL-A13J         TCGA-BT-A0S7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A0YX         TCGA-BT-A20J         TCGA-BT-A20N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A20O         TCGA-BT-A20P         TCGA-BT-A20Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A20R         TCGA-BT-A20T         TCGA-BT-A20U 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A20V         TCGA-BT-A20W         TCGA-BT-A20X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A2LA         TCGA-BT-A2LB         TCGA-C4-A0F0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C4-A0F6         TCGA-CF-A1HR         TCGA-CF-A1HS 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CF-A27C         TCGA-CU-A0YN         TCGA-DK-A1A3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DK-A1A5         TCGA-DK-A1A6         TCGA-DK-A1AA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DK-A1AB         TCGA-DK-A1AC         TCGA-DK-A1AD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HQ-A2OE 
"17P GAIN WILD-TYPE" 
D30V4, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 49 
        TCGA-BL-A13I         TCGA-BL-A13J         TCGA-BT-A0S7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A0YX         TCGA-BT-A20J         TCGA-BT-A20N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A20O         TCGA-BT-A20P         TCGA-BT-A20Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A20R         TCGA-BT-A20T         TCGA-BT-A20U 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A20V         TCGA-BT-A20W         TCGA-BT-A20X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A2LA         TCGA-BT-A2LB         TCGA-C4-A0F0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C4-A0F6         TCGA-CF-A1HR         TCGA-CF-A1HS 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CF-A27C         TCGA-CU-A0YN         TCGA-DK-A1A3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DK-A1A5         TCGA-DK-A1A6         TCGA-DK-A1AA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DK-A1AB         TCGA-DK-A1AC         TCGA-DK-A1AD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HQ-A2OE 
"17P GAIN WILD-TYPE" 
D30V5, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                4                 46
  CLUS_2                1                 32
  CLUS_3                3                 35
D30V6, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                 36
  CLUS_2                2                 16
  CLUS_3                3                 61
D30V7, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                 33
  CLUS_2                5                 63
  CLUS_3                1                 45
D30V8, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                  7
  CLUS_2                2                 30
  CLUS_3                5                104

Clustering(31) Variable = 17q gain mutation analysis
D31V1, multiclass
D31V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               10                 26
  CLUS_2                3                 47
  CLUS_3               10                 29
  CLUS_4                2                 23
D31V3, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                  8
  CLUS_2                2                  8
  CLUS_3                2                 12
  CLUS_4                1                 15
D31V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                 13
  CLUS_2                2                 12
  CLUS_3                6                 18
D31V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               13                 37
  CLUS_2                2                 31
  CLUS_3                3                 35
D31V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                 37
  CLUS_2                3                 15
  CLUS_3               13                 51
D31V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                9                 26
  CLUS_2               11                 57
  CLUS_3                4                 42
D31V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                  7
  CLUS_2                9                 23
  CLUS_3               14                 95

Clustering(32) Variable = 18p gain mutation analysis
D32V1, multiclass
D32V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                8                 28
  CLUS_2                9                 41
  CLUS_3                8                 31
  CLUS_4                1                 24
D32V3, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                1                  9
  CLUS_3                1                 13
  CLUS_4                2                 14
D32V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                3                 11
  CLUS_3                1                 23
D32V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                7                 43
  CLUS_2                2                 31
  CLUS_3               10                 28
D32V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                8                 31
  CLUS_2                3                 15
  CLUS_3                8                 56
D32V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                8                 27
  CLUS_2               12                 56
  CLUS_3                5                 41
D32V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                  6
  CLUS_2                9                 23
  CLUS_3               14                 95

Clustering(33) Variable = 18q gain mutation analysis
D33V1, multiclass
D33V2, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                 34
  CLUS_2                4                 46
  CLUS_3                3                 36
  CLUS_4                0                 25
D33V3, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                0                 10
  CLUS_3                0                 14
  CLUS_4                2                 14
D33V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                1                 13
  CLUS_3                0                 24
D33V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 49
  CLUS_2                2                 31
  CLUS_3                3                 35
D33V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                 37
  CLUS_2                2                 16
  CLUS_3                2                 62
D33V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 34
  CLUS_2                4                 64
  CLUS_3                3                 43
D33V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                  7
  CLUS_2                1                 31
  CLUS_3                6                103

Clustering(34) Variable = 19p gain mutation analysis
D34V1, multiclass
D34V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                4                 32
  CLUS_2                1                 49
  CLUS_3                7                 32
  CLUS_4                3                 22
D34V3, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2I1         TCGA-DK-A2I2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HQ-A2OE 
"19P GAIN WILD-TYPE" 
D34V4, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2I1         TCGA-DK-A2I2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HQ-A2OE 
"19P GAIN WILD-TYPE" 
D34V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                8                 42
  CLUS_2                3                 30
  CLUS_3                1                 37
D34V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 37
  CLUS_2                2                 16
  CLUS_3                8                 56
D34V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                4                 31
  CLUS_2                9                 59
  CLUS_3                2                 44
D34V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                  7
  CLUS_2                4                 28
  CLUS_3               10                 99

Clustering(35) Variable = 19q gain mutation analysis
D35V1, multiclass
D35V2, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               11                 25
  CLUS_2                5                 45
  CLUS_3                8                 31
  CLUS_4                5                 20
D35V3, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                1                  9
  CLUS_3                2                 12
  CLUS_4                5                 11
D35V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 11
  CLUS_2                3                 11
  CLUS_3                5                 19
D35V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1               16                 34
  CLUS_2                6                 27
  CLUS_3                4                 34
D35V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                4                 35
  CLUS_2                5                 13
  CLUS_3               17                 47
D35V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                5                 30
  CLUS_2               17                 51
  CLUS_3                7                 39
D35V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                  6
  CLUS_2                5                 27
  CLUS_3               22                 87

Clustering(36) Variable = 20p gain mutation analysis
D36V1, multiclass
D36V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               16                 20
  CLUS_2               11                 39
  CLUS_3               17                 22
  CLUS_4               10                 15
D36V3, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                6                  5
  CLUS_2                4                  6
  CLUS_3                4                 10
  CLUS_4                4                 12
D36V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                4                  9
  CLUS_2                6                  8
  CLUS_3                8                 16
D36V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               22                 28
  CLUS_2               14                 19
  CLUS_3               12                 26
D36V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               14                 25
  CLUS_2                4                 14
  CLUS_3               30                 34
D36V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               15                 20
  CLUS_2               25                 43
  CLUS_3               13                 33
D36V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                4                  4
  CLUS_2               13                 19
  CLUS_3               36                 73

Clustering(37) Variable = 20q gain mutation analysis
D37V1, multiclass
D37V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               17                 19
  CLUS_2               12                 38
  CLUS_3               19                 20
  CLUS_4               11                 14
D37V3, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                6                  5
  CLUS_2                3                  7
  CLUS_3                6                  8
  CLUS_4                4                 12
D37V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                6                  8
  CLUS_3               10                 14
D37V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               25                 25
  CLUS_2               13                 20
  CLUS_3               10                 28
D37V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               13                 26
  CLUS_2                4                 14
  CLUS_3               31                 33
D37V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               18                 17
  CLUS_2               29                 39
  CLUS_3               11                 35
D37V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                  4
  CLUS_2               16                 16
  CLUS_3               38                 71

Clustering(38) Variable = 21q gain mutation analysis
D38V1, multiclass
D38V2, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               15                 21
  CLUS_2                5                 45
  CLUS_3                5                 34
  CLUS_4                2                 23
D38V3, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                  8
  CLUS_2                3                  7
  CLUS_3                2                 12
  CLUS_4                2                 14
D38V4, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                3                 11
  CLUS_3                6                 18
D38V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1               13                 37
  CLUS_2                6                 27
  CLUS_3                4                 34
D38V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                4                 35
  CLUS_2                2                 16
  CLUS_3               17                 47
D38V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                9                 26
  CLUS_2                9                 59
  CLUS_3                9                 37
D38V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                  8
  CLUS_2                9                 23
  CLUS_3               18                 91

Clustering(39) Variable = 22q gain mutation analysis
D39V1, multiclass
D39V2, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                3                 33
  CLUS_2                3                 47
  CLUS_3                6                 33
  CLUS_4                0                 25
D39V3, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                0                 10
  CLUS_3                2                 12
  CLUS_4                2                 14
D39V4, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                0                 14
  CLUS_3                3                 21
D39V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                5                 45
  CLUS_2                1                 32
  CLUS_3                4                 34
D39V6, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                4                 35
  CLUS_2                1                 17
  CLUS_3                5                 59
D39V7, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                3                 32
  CLUS_2                9                 59
  CLUS_3                0                 46
D39V8, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                0                  8
  CLUS_2                3                 29
  CLUS_3                9                100

Clustering(40) Variable = Xq gain mutation analysis
D40V1, multiclass
D40V2, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                34
  CLUS_2               2                48
  CLUS_3               2                37
  CLUS_4               0                25
D40V3, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                50 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BT-A0S7        TCGA-BT-A0YX 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O        TCGA-BT-A20P 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T        TCGA-BT-A20U 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X        TCGA-BT-A2LA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0        TCGA-C4-A0F6 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C        TCGA-CU-A0YN 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6        TCGA-DK-A1AA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD        TCGA-DK-A1AE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-H4-A2HQ        TCGA-HQ-A2OE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D40V4, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                50 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BT-A0S7        TCGA-BT-A0YX 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O        TCGA-BT-A20P 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T        TCGA-BT-A20U 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X        TCGA-BT-A2LA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0        TCGA-C4-A0F6 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C        TCGA-CU-A0YN 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6        TCGA-DK-A1AA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD        TCGA-DK-A1AE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-H4-A2HQ        TCGA-HQ-A2OE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D40V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               3                47
  CLUS_2               2                31
  CLUS_3               1                37
D40V6, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                37
  CLUS_2               1                17
  CLUS_3               3                61
D40V7, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                34
  CLUS_2               3                65
  CLUS_3               2                44
D40V8, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               1                31
  CLUS_3               5               104

Clustering(41) Variable = 1p loss mutation analysis
D41V1, multiclass
D41V2, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0                36
  CLUS_2               0                50
  CLUS_3               2                37
  CLUS_4               2                23
D41V3, multiclass
D41V4, multiclass
D41V5, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2               119 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BL-A3JM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BT-A0S7        TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BT-A20O        TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BT-A20T        TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BT-A20X        TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-BT-A2LD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BT-A3PH        TCGA-BT-A3PJ        TCGA-BT-A3PK        TCGA-C4-A0F0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CF-A3MF        TCGA-CF-A3MG        TCGA-CF-A3MH        TCGA-CF-A3MI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-CU-A0YO        TCGA-CU-A3KJ        TCGA-CU-A3QU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CU-A3YL        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DK-A1A7        TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DK-A1AD        TCGA-DK-A1AE        TCGA-DK-A1AF        TCGA-DK-A1AG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DK-A2HX        TCGA-DK-A2I1        TCGA-DK-A2I2        TCGA-DK-A2I4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DK-A2I6        TCGA-DK-A3IK        TCGA-DK-A3IL        TCGA-DK-A3IM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DK-A3IN        TCGA-DK-A3IS        TCGA-DK-A3IT        TCGA-DK-A3IU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DK-A3IV        TCGA-DK-A3WX        TCGA-DK-A3WY        TCGA-DK-A3X1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DK-A3X2        TCGA-E5-A2PC        TCGA-E7-A3X6        TCGA-E7-A3Y1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FD-A3B3        TCGA-FD-A3B4        TCGA-FD-A3B5        TCGA-FD-A3B6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FD-A3B7        TCGA-FD-A3B8        TCGA-FD-A3N5        TCGA-FD-A3N6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FD-A3NA        TCGA-FD-A3SJ        TCGA-FD-A3SL        TCGA-FD-A3SM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FD-A3SN        TCGA-FD-A3SO        TCGA-FD-A3SP        TCGA-FD-A3SQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FD-A3SR        TCGA-FD-A3SS        TCGA-FT-A3EE        TCGA-G2-A2EF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL        TCGA-G2-A2EO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G2-A2ES        TCGA-G2-A3IB        TCGA-G2-A3IE        TCGA-G2-A3VY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GC-A3BM        TCGA-GC-A3I6        TCGA-GC-A3OO        TCGA-GC-A3RB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GC-A3RC        TCGA-GC-A3RD        TCGA-GC-A3WC        TCGA-GD-A2C5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GD-A3OP        TCGA-GD-A3OQ        TCGA-GD-A3OS        TCGA-GV-A3JV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GV-A3JW        TCGA-GV-A3JX        TCGA-GV-A3JZ        TCGA-GV-A3QF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GV-A3QG        TCGA-GV-A3QH        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-HQ-A2OE        TCGA-K4-A3WS        TCGA-K4-A3WV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D41V6, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2               119 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BL-A3JM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BT-A0S7        TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BT-A20O        TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BT-A20T        TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BT-A20X        TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-BT-A2LD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BT-A3PH        TCGA-BT-A3PJ        TCGA-BT-A3PK        TCGA-C4-A0F0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CF-A3MF        TCGA-CF-A3MG        TCGA-CF-A3MH        TCGA-CF-A3MI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-CU-A0YO        TCGA-CU-A3KJ        TCGA-CU-A3QU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CU-A3YL        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DK-A1A7        TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DK-A1AD        TCGA-DK-A1AE        TCGA-DK-A1AF        TCGA-DK-A1AG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DK-A2HX        TCGA-DK-A2I1        TCGA-DK-A2I2        TCGA-DK-A2I4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DK-A2I6        TCGA-DK-A3IK        TCGA-DK-A3IL        TCGA-DK-A3IM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DK-A3IN        TCGA-DK-A3IS        TCGA-DK-A3IT        TCGA-DK-A3IU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DK-A3IV        TCGA-DK-A3WX        TCGA-DK-A3WY        TCGA-DK-A3X1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DK-A3X2        TCGA-E5-A2PC        TCGA-E7-A3X6        TCGA-E7-A3Y1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FD-A3B3        TCGA-FD-A3B4        TCGA-FD-A3B5        TCGA-FD-A3B6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FD-A3B7        TCGA-FD-A3B8        TCGA-FD-A3N5        TCGA-FD-A3N6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FD-A3NA        TCGA-FD-A3SJ        TCGA-FD-A3SL        TCGA-FD-A3SM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FD-A3SN        TCGA-FD-A3SO        TCGA-FD-A3SP        TCGA-FD-A3SQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FD-A3SR        TCGA-FD-A3SS        TCGA-FT-A3EE        TCGA-G2-A2EF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL        TCGA-G2-A2EO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G2-A2ES        TCGA-G2-A3IB        TCGA-G2-A3IE        TCGA-G2-A3VY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GC-A3BM        TCGA-GC-A3I6        TCGA-GC-A3OO        TCGA-GC-A3RB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GC-A3RC        TCGA-GC-A3RD        TCGA-GC-A3WC        TCGA-GD-A2C5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GD-A3OP        TCGA-GD-A3OQ        TCGA-GD-A3OS        TCGA-GV-A3JV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GV-A3JW        TCGA-GV-A3JX        TCGA-GV-A3JZ        TCGA-GV-A3QF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GV-A3QG        TCGA-GV-A3QH        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-HQ-A2OE        TCGA-K4-A3WS        TCGA-K4-A3WV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D41V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                34
  CLUS_2               3                65
  CLUS_3               0                46
D41V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               0                32
  CLUS_3               3               106

Clustering(42) Variable = 2p loss mutation analysis
D42V1, multiclass
D42V2, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                36
  CLUS_2               1                49
  CLUS_3               3                36
  CLUS_4               4                21
D42V3, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                49 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DK-A1AE        TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2I1 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HQ-A2OE 
"2P LOSS WILD-TYPE" 
D42V4, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                49 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DK-A1AE        TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2I1 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HQ-A2OE 
"2P LOSS WILD-TYPE" 
D42V5, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               5                45
  CLUS_2               1                32
  CLUS_3               1                37
D42V6, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                39
  CLUS_2               1                17
  CLUS_3               6                58
D42V7, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               2                33
  CLUS_2               4                64
  CLUS_3               2                44
D42V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               2                30
  CLUS_3               6               103

Clustering(43) Variable = 2q loss mutation analysis
D43V1, multiclass
D43V2, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               5                31
  CLUS_2               3                47
  CLUS_3               6                33
  CLUS_4               3                22
D43V3, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                10
  CLUS_2               1                 9
  CLUS_3               1                13
  CLUS_4               2                14
D43V4, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               0                14
  CLUS_3               4                20
D43V5, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               9                41
  CLUS_2               3                30
  CLUS_3               4                34
D43V6, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                38
  CLUS_2               3                15
  CLUS_3              12                52
D43V7, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               4                31
  CLUS_2               9                59
  CLUS_3               4                42
D43V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               5                27
  CLUS_3              12                97

Clustering(44) Variable = 3p loss mutation analysis
D44V1, multiclass
D44V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                35
  CLUS_2               4                46
  CLUS_3               3                36
  CLUS_4               1                24
D44V3, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                11
  CLUS_2               0                10
  CLUS_3               1                13
  CLUS_4               3                13
D44V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               1                13
  CLUS_3               1                23
D44V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                48
  CLUS_2               1                32
  CLUS_3               6                32
D44V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               6                33
  CLUS_2               1                17
  CLUS_3               2                62
D44V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                35
  CLUS_2               6                62
  CLUS_3               3                43
D44V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               0                32
  CLUS_3               8               101

Clustering(45) Variable = 4p loss mutation analysis
D45V1, multiclass
D45V2, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               9                27
  CLUS_2               6                44
  CLUS_3              10                29
  CLUS_4               4                21
D45V3, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               1                10
  CLUS_2               1                 9
  CLUS_3               3                11
  CLUS_4               2                14
D45V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               1                13
  CLUS_3               4                20
D45V5, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              11                39
  CLUS_2               4                29
  CLUS_3               9                29
D45V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               5                34
  CLUS_2               3                15
  CLUS_3              16                48
D45V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               6                29
  CLUS_2              16                52
  CLUS_3               7                39
D45V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                 6
  CLUS_2               5                27
  CLUS_3              22                87

Clustering(46) Variable = 4q loss mutation analysis
D46V1, multiclass
D46V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               8                28
  CLUS_2               9                41
  CLUS_3               6                33
  CLUS_4               3                22
D46V3, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               2                 8
  CLUS_3               3                11
  CLUS_4               1                15
D46V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                12
  CLUS_2               2                12
  CLUS_3               5                19
D46V5, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               9                41
  CLUS_2               4                29
  CLUS_3               8                30
D46V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               5                34
  CLUS_2               4                14
  CLUS_3              12                52
D46V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               5                30
  CLUS_2              14                54
  CLUS_3               7                39
D46V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               3                 5
  CLUS_2               4                28
  CLUS_3              19                90

Clustering(47) Variable = 5p loss mutation analysis
D47V1, multiclass
D47V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               5                31
  CLUS_2               5                45
  CLUS_3               2                37
  CLUS_4               2                23
D47V3, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                10
  CLUS_2               0                10
  CLUS_3               3                11
  CLUS_4               2                14
D47V4, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               1                13
  CLUS_3               3                21
D47V5, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               7                43
  CLUS_2               2                31
  CLUS_3               4                34
D47V6, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                36
  CLUS_2               2                16
  CLUS_3               8                56
D47V7, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2                33
  CLUS_2               9                59
  CLUS_3               3                43
D47V8, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               2                30
  CLUS_3              11                98

Clustering(48) Variable = 5q loss mutation analysis
D48V1, multiclass
D48V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              14                22
  CLUS_2              10                40
  CLUS_3               9                30
  CLUS_4               3                22
D48V3, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               1                 9
  CLUS_3               4                10
  CLUS_4               3                13
D48V4, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3                10
  CLUS_2               2                12
  CLUS_3               5                19
D48V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              13                37
  CLUS_2               7                26
  CLUS_3              10                28
D48V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              10                29
  CLUS_2               3                15
  CLUS_3              17                47
D48V7, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              10                25
  CLUS_2              18                50
  CLUS_3               8                38
D48V8, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               3                 5
  CLUS_2              10                22
  CLUS_3              23                86

Clustering(49) Variable = 6p loss mutation analysis
D49V1, multiclass
D49V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               7                29
  CLUS_2               3                47
  CLUS_3               4                35
  CLUS_4               4                21
D49V3, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                11
  CLUS_2               0                10
  CLUS_3               3                11
  CLUS_4               3                13
D49V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3                10
  CLUS_2               1                13
  CLUS_3               2                22
D49V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               8                42
  CLUS_2               2                31
  CLUS_3               6                32
D49V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               4                35
  CLUS_2               2                16
  CLUS_3              10                54
D49V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3                32
  CLUS_2               8                60
  CLUS_3               7                39
D49V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               3                29
  CLUS_3              14                95

Clustering(50) Variable = 6q loss mutation analysis
D50V1, multiclass
D50V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              12                24
  CLUS_2               3                47
  CLUS_3               8                31
  CLUS_4               6                19
D50V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                10
  CLUS_2               0                10
  CLUS_3               4                10
  CLUS_4               4                12
D50V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3                10
  CLUS_2               2                12
  CLUS_3               4                20
D50V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              15                35
  CLUS_2               5                28
  CLUS_3               7                31
D50V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               5                34
  CLUS_2               2                16
  CLUS_3              20                44
D50V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6                29
  CLUS_2              15                53
  CLUS_3               8                38
D50V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               6                26
  CLUS_3              22                87

Clustering(51) Variable = 7q loss mutation analysis
D51V1, multiclass
D51V2, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1                35
  CLUS_2               0                50
  CLUS_3               2                37
  CLUS_4               0                25
D51V3, multiclass
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                50 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-DK-A1A3        TCGA-DK-A1A6        TCGA-DK-A1AA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD        TCGA-DK-A1AE 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-H4-A2HQ        TCGA-HQ-A2OE 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
D51V4, multiclass
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                50 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-DK-A1A3        TCGA-DK-A1A6        TCGA-DK-A1AA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD        TCGA-DK-A1AE 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-H4-A2HQ        TCGA-HQ-A2OE 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
D51V5, multiclass
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2               119 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BL-A3JM 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A0S7        TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A20O        TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A20T        TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A20X        TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-BT-A2LD 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A3PH        TCGA-BT-A3PJ        TCGA-BT-A3PK        TCGA-C4-A0F0 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CF-A3MF        TCGA-CF-A3MG        TCGA-CF-A3MH        TCGA-CF-A3MI 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-CU-A0YO        TCGA-CU-A0YR        TCGA-CU-A3KJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CU-A3QU        TCGA-CU-A3YL        TCGA-DK-A1A3        TCGA-DK-A1A6 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A1A7        TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A1AD        TCGA-DK-A1AE        TCGA-DK-A1AF        TCGA-DK-A1AG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A2HX        TCGA-DK-A2I1        TCGA-DK-A2I2        TCGA-DK-A2I4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A2I6        TCGA-DK-A3IL        TCGA-DK-A3IM        TCGA-DK-A3IN 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A3IS        TCGA-DK-A3IT        TCGA-DK-A3IU        TCGA-DK-A3IV 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A3WX        TCGA-DK-A3WY        TCGA-DK-A3X1        TCGA-DK-A3X2 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-E5-A2PC        TCGA-E7-A3X6        TCGA-E7-A3Y1        TCGA-FD-A3B3 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FD-A3B4        TCGA-FD-A3B5        TCGA-FD-A3B6        TCGA-FD-A3B7 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FD-A3B8        TCGA-FD-A3N5        TCGA-FD-A3N6        TCGA-FD-A3NA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FD-A3SJ        TCGA-FD-A3SL        TCGA-FD-A3SM        TCGA-FD-A3SN 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FD-A3SO        TCGA-FD-A3SP        TCGA-FD-A3SQ        TCGA-FD-A3SR 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FD-A3SS        TCGA-FT-A3EE        TCGA-G2-A2EF        TCGA-G2-A2EJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G2-A2EK        TCGA-G2-A2EL        TCGA-G2-A2EO        TCGA-G2-A2ES 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G2-A3IB        TCGA-G2-A3IE        TCGA-G2-A3VY        TCGA-GC-A3BM 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GC-A3I6        TCGA-GC-A3OO        TCGA-GC-A3RB        TCGA-GC-A3RC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GC-A3RD        TCGA-GC-A3WC        TCGA-GD-A2C5        TCGA-GD-A3OP 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GD-A3OQ        TCGA-GD-A3OS        TCGA-GV-A3JV        TCGA-GV-A3JW 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GV-A3JX        TCGA-GV-A3JZ        TCGA-GV-A3QF        TCGA-GV-A3QG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GV-A3QH        TCGA-GV-A3QI        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HQ-A2OE        TCGA-K4-A3WS        TCGA-K4-A3WV 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
D51V6, multiclass
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2               119 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BL-A3JM 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A0S7        TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A20O        TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A20T        TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A20X        TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-BT-A2LD 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A3PH        TCGA-BT-A3PJ        TCGA-BT-A3PK        TCGA-C4-A0F0 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CF-A3MF        TCGA-CF-A3MG        TCGA-CF-A3MH        TCGA-CF-A3MI 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-CU-A0YO        TCGA-CU-A0YR        TCGA-CU-A3KJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CU-A3QU        TCGA-CU-A3YL        TCGA-DK-A1A3        TCGA-DK-A1A6 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A1A7        TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A1AD        TCGA-DK-A1AE        TCGA-DK-A1AF        TCGA-DK-A1AG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A2HX        TCGA-DK-A2I1        TCGA-DK-A2I2        TCGA-DK-A2I4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A2I6        TCGA-DK-A3IL        TCGA-DK-A3IM        TCGA-DK-A3IN 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A3IS        TCGA-DK-A3IT        TCGA-DK-A3IU        TCGA-DK-A3IV 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A3WX        TCGA-DK-A3WY        TCGA-DK-A3X1        TCGA-DK-A3X2 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-E5-A2PC        TCGA-E7-A3X6        TCGA-E7-A3Y1        TCGA-FD-A3B3 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FD-A3B4        TCGA-FD-A3B5        TCGA-FD-A3B6        TCGA-FD-A3B7 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FD-A3B8        TCGA-FD-A3N5        TCGA-FD-A3N6        TCGA-FD-A3NA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FD-A3SJ        TCGA-FD-A3SL        TCGA-FD-A3SM        TCGA-FD-A3SN 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FD-A3SO        TCGA-FD-A3SP        TCGA-FD-A3SQ        TCGA-FD-A3SR 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FD-A3SS        TCGA-FT-A3EE        TCGA-G2-A2EF        TCGA-G2-A2EJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G2-A2EK        TCGA-G2-A2EL        TCGA-G2-A2EO        TCGA-G2-A2ES 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G2-A3IB        TCGA-G2-A3IE        TCGA-G2-A3VY        TCGA-GC-A3BM 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GC-A3I6        TCGA-GC-A3OO        TCGA-GC-A3RB        TCGA-GC-A3RC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GC-A3RD        TCGA-GC-A3WC        TCGA-GD-A2C5        TCGA-GD-A3OP 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GD-A3OQ        TCGA-GD-A3OS        TCGA-GV-A3JV        TCGA-GV-A3JW 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GV-A3JX        TCGA-GV-A3JZ        TCGA-GV-A3QF        TCGA-GV-A3QG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GV-A3QH        TCGA-GV-A3QI        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HQ-A2OE        TCGA-K4-A3WS        TCGA-K4-A3WV 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
D51V7, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               2                33
  CLUS_2               1                67
  CLUS_3               0                46
D51V8, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               2                30
  CLUS_3               1               108

Clustering(52) Variable = 8p loss mutation analysis
D52V1, multiclass
D52V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              23                13
  CLUS_2              15                35
  CLUS_3               5                34
  CLUS_4               6                19
D52V3, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               5                 6
  CLUS_2               4                 6
  CLUS_3               2                12
  CLUS_4               2                14
D52V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               2                11
  CLUS_2               6                 8
  CLUS_3               5                19
D52V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              18                32
  CLUS_2              11                22
  CLUS_3              10                28
D52V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              10                29
  CLUS_2               5                13
  CLUS_3              24                40
D52V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              19                16
  CLUS_2              16                52
  CLUS_3              13                33
D52V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               3                 5
  CLUS_2              18                14
  CLUS_3              27                82

Clustering(53) Variable = 8q loss mutation analysis
D53V1, multiclass
D53V2, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3                33
  CLUS_2               2                48
  CLUS_3               0                39
  CLUS_4               0                25
D53V3, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                50 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DK-A1AE        TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DK-A2I1        TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FD-A3B4        TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G2-A2EL        TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-GD-A2C5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-H4-A2HO        TCGA-HQ-A2OE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D53V4, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                50 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DK-A1AE        TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DK-A2I1        TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FD-A3B4        TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G2-A2EL        TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-GD-A2C5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-H4-A2HO        TCGA-HQ-A2OE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D53V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2                48
  CLUS_2               0                33
  CLUS_3               1                37
D53V6, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                38
  CLUS_2               0                18
  CLUS_3               2                62
D53V7, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3                32
  CLUS_2               1                67
  CLUS_3               1                45
D53V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               3                29
  CLUS_3               1               108

Clustering(54) Variable = 9p loss mutation analysis
D54V1, multiclass
D54V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              11                25
  CLUS_2               6                44
  CLUS_3              16                23
  CLUS_4              10                15
D54V3, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                10
  CLUS_2               3                 7
  CLUS_3               9                 5
  CLUS_4               5                11
D54V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               3                10
  CLUS_2               4                10
  CLUS_3              11                13
D54V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              22                28
  CLUS_2               6                27
  CLUS_3              10                28
D54V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               8                31
  CLUS_2               1                17
  CLUS_3              29                35
D54V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               9                26
  CLUS_2              21                47
  CLUS_3              13                33
D54V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               2                 6
  CLUS_2               7                25
  CLUS_3              34                75

Clustering(55) Variable = 9q loss mutation analysis
D55V1, multiclass
D55V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               9                27
  CLUS_2               6                44
  CLUS_3              17                22
  CLUS_4               9                16
D55V3, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               0                10
  CLUS_3              10                 4
  CLUS_4               5                11
D55V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               3                10
  CLUS_2               1                13
  CLUS_3              13                11
D55V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              23                27
  CLUS_2               5                28
  CLUS_3               7                31
D55V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               4                35
  CLUS_2               2                16
  CLUS_3              29                35
D55V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              10                25
  CLUS_2              20                48
  CLUS_3              11                35
D55V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                 7
  CLUS_2               9                23
  CLUS_3              31                78

Clustering(56) Variable = 10p loss mutation analysis
D56V1, multiclass
D56V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                5                 31
  CLUS_2                6                 44
  CLUS_3                6                 33
  CLUS_4                2                 23
D56V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                3                  8
  CLUS_2                1                  9
  CLUS_3                0                 14
  CLUS_4                2                 14
D56V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                3                 11
  CLUS_3                2                 22
D56V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                5                 45
  CLUS_2                3                 30
  CLUS_3                8                 30
D56V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                8                 31
  CLUS_2                2                 16
  CLUS_3                6                 58
D56V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                5                 30
  CLUS_2               11                 57
  CLUS_3                3                 43
D56V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                3                  5
  CLUS_2                5                 27
  CLUS_3               11                 98

Clustering(57) Variable = 10q loss mutation analysis
D57V1, multiclass
D57V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               12                 24
  CLUS_2                5                 45
  CLUS_3                9                 30
  CLUS_4                4                 21
D57V3, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                1                  9
  CLUS_3                2                 12
  CLUS_4                1                 15
D57V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                2                 12
  CLUS_3                2                 22
D57V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               14                 36
  CLUS_2                4                 29
  CLUS_3                7                 31
D57V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                9                 30
  CLUS_2                0                 18
  CLUS_3               16                 48
D57V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               10                 25
  CLUS_2               16                 52
  CLUS_3                4                 42
D57V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                4                  4
  CLUS_2               10                 22
  CLUS_3               16                 93

Clustering(58) Variable = 11p loss mutation analysis
D58V1, multiclass
D58V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               12                 24
  CLUS_2                7                 43
  CLUS_3               20                 19
  CLUS_4                9                 16
D58V3, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                3                  7
  CLUS_3                8                  6
  CLUS_4                7                  9
D58V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                  7
  CLUS_2                4                 10
  CLUS_3               10                 14
D58V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               21                 29
  CLUS_2                6                 27
  CLUS_3               13                 25
D58V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               10                 29
  CLUS_2                1                 17
  CLUS_3               29                 35
D58V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               14                 21
  CLUS_2               23                 45
  CLUS_3               10                 36
D58V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                  6
  CLUS_2               12                 20
  CLUS_3               33                 76

Clustering(59) Variable = 11q loss mutation analysis
D59V1, multiclass
D59V2, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                7                 29
  CLUS_2                9                 41
  CLUS_3               16                 23
  CLUS_4                3                 22
D59V3, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                2                  8
  CLUS_3                5                  9
  CLUS_4                8                  8
D59V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                6                  7
  CLUS_2                4                 10
  CLUS_3                7                 17
D59V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               14                 36
  CLUS_2                4                 29
  CLUS_3               10                 28
D59V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                9                 30
  CLUS_2                2                 16
  CLUS_3               17                 47
D59V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                8                 27
  CLUS_2               19                 49
  CLUS_3                7                 39
D59V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                  7
  CLUS_2                9                 23
  CLUS_3               24                 85

Clustering(60) Variable = 12p loss mutation analysis
D60V1, multiclass
D60V2, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                3                 33
  CLUS_2                0                 50
  CLUS_3                2                 37
  CLUS_4                1                 24
D60V3, multiclass
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 50 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2HX         TCGA-DK-A2I1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A2I2         TCGA-E5-A2PC         TCGA-FD-A3B3 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FD-A3B4         TCGA-G2-A2EF         TCGA-G2-A2EJ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G2-A2EK         TCGA-G2-A2EL         TCGA-G2-A2EO 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G2-A2ES         TCGA-GD-A2C5         TCGA-H4-A2HO 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-H4-A2HQ         TCGA-HQ-A2OE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D60V4, multiclass
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 50 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2HX         TCGA-DK-A2I1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A2I2         TCGA-E5-A2PC         TCGA-FD-A3B3 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FD-A3B4         TCGA-G2-A2EF         TCGA-G2-A2EJ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G2-A2EK         TCGA-G2-A2EL         TCGA-G2-A2EO 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G2-A2ES         TCGA-GD-A2C5         TCGA-H4-A2HO 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-H4-A2HQ         TCGA-HQ-A2OE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D60V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                3                 47
  CLUS_2                2                 31
  CLUS_3                0                 38
D60V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 39
  CLUS_2                1                 17
  CLUS_3                4                 60
D60V7, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 34
  CLUS_2                4                 64
  CLUS_3                1                 45
D60V8, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                  8
  CLUS_2                1                 31
  CLUS_3                5                104

Clustering(61) Variable = 12q loss mutation analysis
D61V1, multiclass
D61V2, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                2                 34
  CLUS_2                3                 47
  CLUS_3                3                 36
  CLUS_4                1                 24
D61V3, multiclass
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LA         TCGA-BT-A2LB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C4-A0EZ         TCGA-C4-A0F6         TCGA-CF-A1HR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-DK-A1A3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A1A5         TCGA-DK-A1A6         TCGA-DK-A1AA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A1AB         TCGA-DK-A1AC         TCGA-DK-A1AD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-HQ-A2OE 
"12Q LOSS WILD-TYPE" 
D61V4, multiclass
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LA         TCGA-BT-A2LB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C4-A0EZ         TCGA-C4-A0F6         TCGA-CF-A1HR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-DK-A1A3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A1A5         TCGA-DK-A1A6         TCGA-DK-A1AA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A1AB         TCGA-DK-A1AC         TCGA-DK-A1AD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-HQ-A2OE 
"12Q LOSS WILD-TYPE" 
D61V5, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                4                 46
  CLUS_2                0                 33
  CLUS_3                4                 34
D61V6, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                4                 35
  CLUS_2                0                 18
  CLUS_3                4                 60
D61V7, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                2                 33
  CLUS_2                6                 62
  CLUS_3                1                 45
D61V8, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                1                  7
  CLUS_2                2                 30
  CLUS_3                6                103

Clustering(62) Variable = 13q loss mutation analysis
D62V1, multiclass
D62V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                4                 32
  CLUS_2                7                 43
  CLUS_3                8                 31
  CLUS_4                1                 24
D62V3, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                2                  8
  CLUS_3                2                 12
  CLUS_4                6                 10
D62V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                5                  8
  CLUS_2                1                 13
  CLUS_3                4                 20
D62V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                4                 46
  CLUS_2                4                 29
  CLUS_3                9                 29
D62V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                6                 33
  CLUS_2                4                 14
  CLUS_3                7                 57
D62V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                6                 29
  CLUS_2                9                 59
  CLUS_3                5                 41
D62V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                  6
  CLUS_2                5                 27
  CLUS_3               13                 96

Clustering(63) Variable = 14q loss mutation analysis
D63V1, multiclass
D63V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               12                 24
  CLUS_2                5                 45
  CLUS_3                6                 33
  CLUS_4                2                 23
D63V3, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                2                  8
  CLUS_3                3                 11
  CLUS_4                4                 12
D63V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                4                  9
  CLUS_2                1                 13
  CLUS_3                5                 19
D63V5, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               10                 40
  CLUS_2                5                 28
  CLUS_3                5                 33
D63V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                4                 35
  CLUS_2                3                 15
  CLUS_3               13                 51
D63V7, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               11                 24
  CLUS_2                8                 60
  CLUS_3                6                 40
D63V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                2                  6
  CLUS_2                8                 24
  CLUS_3               15                 94

Clustering(64) Variable = 15q loss mutation analysis
D64V1, multiclass
D64V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                6                 30
  CLUS_2                9                 41
  CLUS_3                4                 35
  CLUS_4                0                 25
D64V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                  7
  CLUS_2                0                 10
  CLUS_3                1                 13
  CLUS_4                3                 13
D64V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                3                 11
  CLUS_3                2                 22
D64V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                6                 44
  CLUS_2                1                 32
  CLUS_3                8                 30
D64V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                9                 30
  CLUS_2                1                 17
  CLUS_3                5                 59
D64V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                3                 32
  CLUS_2               12                 56
  CLUS_3                3                 43
D64V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                  4
  CLUS_2                3                 29
  CLUS_3               11                 98

Clustering(65) Variable = 16p loss mutation analysis
D65V1, multiclass
D65V2, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                7                 29
  CLUS_2                6                 44
  CLUS_3                3                 36
  CLUS_4                1                 24
D65V3, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                2                  8
  CLUS_3                1                 13
  CLUS_4                1                 15
D65V4, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                2                 12
  CLUS_3                3                 21
D65V5, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                4                 46
  CLUS_2                4                 29
  CLUS_3                7                 31
D65V6, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                6                 33
  CLUS_2                2                 16
  CLUS_3                7                 57
D65V7, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                4                 31
  CLUS_2               11                 57
  CLUS_3                2                 44
D65V8, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                4                  4
  CLUS_2                5                 27
  CLUS_3                8                101

Clustering(66) Variable = 16q loss mutation analysis
D66V1, multiclass
D66V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                7                 29
  CLUS_2                4                 46
  CLUS_3                4                 35
  CLUS_4                2                 23
D66V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                2                  8
  CLUS_3                1                 13
  CLUS_4                1                 15
D66V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                1                 13
  CLUS_3                3                 21
D66V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                 45
  CLUS_2                4                 29
  CLUS_3                6                 32
D66V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                4                 35
  CLUS_2                3                 15
  CLUS_3                8                 56
D66V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                 30
  CLUS_2                8                 60
  CLUS_3                4                 42
D66V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                  5
  CLUS_2                6                 26
  CLUS_3                8                101

Clustering(67) Variable = 17p loss mutation analysis
D67V1, multiclass
D67V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                8                 28
  CLUS_2               11                 39
  CLUS_3               11                 28
  CLUS_4               12                 13
D67V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                5                  6
  CLUS_2                2                  8
  CLUS_3                4                 10
  CLUS_4                7                  9
D67V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                  9
  CLUS_2                6                  8
  CLUS_3                8                 16
D67V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               20                 30
  CLUS_2                3                 30
  CLUS_3               12                 26
D67V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               11                 28
  CLUS_2                2                 16
  CLUS_3               22                 42
D67V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                5                 30
  CLUS_2               25                 43
  CLUS_3               12                 34
D67V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                  4
  CLUS_2                4                 28
  CLUS_3               34                 75

Clustering(68) Variable = 17q loss mutation analysis
D68V1, multiclass
D68V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 34
  CLUS_2                0                 50
  CLUS_3                1                 38
  CLUS_4                3                 22
D68V3, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AC         TCGA-DK-A1AD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HQ-A2OE 
"17Q LOSS WILD-TYPE" 
D68V4, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AC         TCGA-DK-A1AD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HQ-A2OE 
"17Q LOSS WILD-TYPE" 
D68V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                 47
  CLUS_2                1                 32
  CLUS_3                1                 37
D68V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 38
  CLUS_2                1                 17
  CLUS_3                3                 61
D68V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 35
  CLUS_2                5                 63
  CLUS_3                1                 45
D68V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                  8
  CLUS_2                0                 32
  CLUS_3                6                103

Clustering(69) Variable = 18p loss mutation analysis
D69V1, multiclass
D69V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                6                 30
  CLUS_2                2                 48
  CLUS_3                9                 30
  CLUS_4                5                 20
D69V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                2                  8
  CLUS_3                2                 12
  CLUS_4                3                 13
D69V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                1                 13
  CLUS_3                3                 21
D69V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                8                 42
  CLUS_2                5                 28
  CLUS_3                6                 32
D69V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                4                 35
  CLUS_2                1                 17
  CLUS_3               14                 50
D69V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 32
  CLUS_2               12                 56
  CLUS_3                7                 39
D69V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                  7
  CLUS_2                0                 32
  CLUS_3               21                 88

Clustering(70) Variable = 18q loss mutation analysis
D70V1, multiclass
D70V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               12                 24
  CLUS_2               11                 39
  CLUS_3               10                 29
  CLUS_4                6                 19
D70V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                  8
  CLUS_2                3                  7
  CLUS_3                2                 12
  CLUS_4                4                 12
D70V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                4                  9
  CLUS_2                5                  9
  CLUS_3                3                 21
D70V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               14                 36
  CLUS_2                5                 28
  CLUS_3               13                 25
D70V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               12                 27
  CLUS_2                3                 15
  CLUS_3               17                 47
D70V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               12                 23
  CLUS_2               17                 51
  CLUS_3               10                 36
D70V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                4                  4
  CLUS_2               10                 22
  CLUS_3               25                 84

Clustering(71) Variable = 19p loss mutation analysis
D71V1, multiclass
D71V2, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 34
  CLUS_2                4                 46
  CLUS_3                2                 37
  CLUS_4                1                 24
D71V3, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                0                 10
  CLUS_3                0                 14
  CLUS_4                1                 15
D71V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                 12
  CLUS_2                2                 12
  CLUS_3                0                 24
D71V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 48
  CLUS_2                1                 32
  CLUS_3                4                 34
D71V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                 35
  CLUS_2                0                 18
  CLUS_3                3                 61
D71V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                3                 32
  CLUS_2                5                 63
  CLUS_3                1                 45
D71V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                  7
  CLUS_2                4                 28
  CLUS_3                4                105

Clustering(72) Variable = 19q loss mutation analysis
D72V1, multiclass
D72V2, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 36
  CLUS_2                2                 48
  CLUS_3                1                 38
  CLUS_4                1                 24
D72V3, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                 50 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LA         TCGA-BT-A2LB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C4-A0EZ         TCGA-C4-A0F0         TCGA-C4-A0F6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CF-A1HR         TCGA-CF-A1HS         TCGA-CF-A27C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2HX         TCGA-DK-A2I1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A2I2         TCGA-E5-A2PC         TCGA-FD-A3B3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FD-A3B4         TCGA-G2-A2EF         TCGA-G2-A2EJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G2-A2EK         TCGA-G2-A2EL         TCGA-G2-A2EO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G2-A2ES         TCGA-GD-A2C5         TCGA-H4-A2HO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-H4-A2HQ         TCGA-HQ-A2OE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D72V4, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                 50 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LA         TCGA-BT-A2LB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C4-A0EZ         TCGA-C4-A0F0         TCGA-C4-A0F6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CF-A1HR         TCGA-CF-A1HS         TCGA-CF-A27C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2HX         TCGA-DK-A2I1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A2I2         TCGA-E5-A2PC         TCGA-FD-A3B3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FD-A3B4         TCGA-G2-A2EF         TCGA-G2-A2EJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G2-A2EK         TCGA-G2-A2EL         TCGA-G2-A2EO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G2-A2ES         TCGA-GD-A2C5         TCGA-H4-A2HO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-H4-A2HQ         TCGA-HQ-A2OE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D72V5, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 49
  CLUS_2                0                 33
  CLUS_3                2                 36
D72V6, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                 37
  CLUS_2                0                 18
  CLUS_3                1                 63
D72V7, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 35
  CLUS_2                4                 64
  CLUS_3                0                 46
D72V8, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                  7
  CLUS_2                1                 31
  CLUS_3                2                107

Clustering(73) Variable = 20p loss mutation analysis
D73V1, multiclass
D73V2, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                 34
  CLUS_2                1                 49
  CLUS_3                1                 38
  CLUS_4                3                 22
D73V3, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20Q 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A20R         TCGA-BT-A20T         TCGA-BT-A20U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A20V         TCGA-BT-A20W         TCGA-BT-A20X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A2LA         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DK-A1A5         TCGA-DK-A1A6         TCGA-DK-A1AA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DK-A1AB         TCGA-DK-A1AC         TCGA-DK-A1AD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HQ-A2OE 
"20P LOSS WILD-TYPE" 
D73V4, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20Q 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A20R         TCGA-BT-A20T         TCGA-BT-A20U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A20V         TCGA-BT-A20W         TCGA-BT-A20X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A2LA         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DK-A1A5         TCGA-DK-A1A6         TCGA-DK-A1AA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DK-A1AB         TCGA-DK-A1AC         TCGA-DK-A1AD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HQ-A2OE 
"20P LOSS WILD-TYPE" 
D73V5, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                 48
  CLUS_2                1                 32
  CLUS_3                2                 36
D73V6, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                 37
  CLUS_2                0                 18
  CLUS_3                3                 61
D73V7, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                 33
  CLUS_2                4                 64
  CLUS_3                1                 45
D73V8, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                  6
  CLUS_2                1                 31
  CLUS_3                4                105

Clustering(74) Variable = 21q loss mutation analysis
D74V1, multiclass
D74V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 34
  CLUS_2                8                 42
  CLUS_3                4                 35
  CLUS_4                3                 22
D74V3, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                0                 10
  CLUS_3                1                 13
  CLUS_4                3                 13
D74V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                2                 12
  CLUS_3                1                 23
D74V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                5                 45
  CLUS_2                3                 30
  CLUS_3                6                 32
D74V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                6                 33
  CLUS_2                1                 17
  CLUS_3                7                 57
D74V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 32
  CLUS_2                9                 59
  CLUS_3                5                 41
D74V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                  6
  CLUS_2                2                 30
  CLUS_3               13                 96

Clustering(75) Variable = 22q loss mutation analysis
D75V1, multiclass
D75V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                9                 27
  CLUS_2               10                 40
  CLUS_3                7                 32
  CLUS_4                3                 22
D75V3, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                4                  7
  CLUS_2                3                  7
  CLUS_3                0                 14
  CLUS_4                3                 13
D75V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                3                 10
  CLUS_2                5                  9
  CLUS_3                2                 22
D75V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                6                 44
  CLUS_2                5                 28
  CLUS_3               12                 26
D75V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               11                 28
  CLUS_2                1                 17
  CLUS_3               11                 53
D75V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                5                 30
  CLUS_2               14                 54
  CLUS_3                9                 37
D75V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                5                  3
  CLUS_2                5                 27
  CLUS_3               18                 91

Clustering(76) Variable = Xq loss mutation analysis
D76V1, multiclass
D76V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                36
  CLUS_2               1                49
  CLUS_3               1                38
  CLUS_4               2                23
D76V3, multiclass
D76V4, multiclass
D76V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                49
  CLUS_2               0                33
  CLUS_3               2                36
D76V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                38
  CLUS_2               1                17
  CLUS_3               1                63
D76V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                35
  CLUS_2               2                66
  CLUS_3               2                44
D76V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                 8
  CLUS_2               0                32
  CLUS_3               4               105
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"             "RPPA_CNMF" 
                     V4                      V5                      V6 
   "RPPA_CHIERARCHICAL"          "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL" 
                     V7                      V8 
          "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
