
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/399194/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SKCM-NRAS_Hotspot_Mutants/3157510/1.GDAC_mergedClustering.Finished/SKCM-NRAS_Hotspot_Mutants.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-NRAS_Hotspot_Mutants", "-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=SKCM-NRAS_Hotspot_Mutants"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=62, in cluster file=62, common to both=62
[1] "Reduce the number of clustering variables from 80 to 67."
[1] 67 62
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                54 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                54 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               29                33 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               29                33 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10                52 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10                52 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               10                52 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               10                52 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                6                56 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                6                56 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                7                55 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                7                55 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                57 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                57 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5                57 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5                57 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                3                59 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                3                59 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               28                34 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               28                34 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3                59 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3                59 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               11                51 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               11                51 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                9                53 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                9                53 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               13                49 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               13                49 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               21                41 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               21                41 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4                58 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4                58 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 57 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 57 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                 57 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                 57 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                 58 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                 58 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                18                 44 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                18                 44 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 5                 57 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 5                 57 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 7                 55 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 7                 55 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 55 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 55 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 56 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 56 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 59 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 59 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 9                 53 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 9                 53 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                 58 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                 58 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 58 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 58 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                 56 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                 56 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                 55 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                 55 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                13                 49 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                13                 49 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                18                 44 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                18                 44 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 9                 53 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 9                 53 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                11                 51 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                11                 51 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                59 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                59 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                58 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                58 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4                58 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4                58 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9                53 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9                53 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10                52 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10                52 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               14                48 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               14                48 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               15                47 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               15                47 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                7                55 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                7                55 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               28                34 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               28                34 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3                59 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3                59 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               11                51 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               11                51 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                59 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                59 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               38                24 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               38                24 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               30                32 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               30                32 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                25                 37 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                25                 37 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                27                 35 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                27                 35 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                19                 43 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                19                 43 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                22                 40 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                22                 40 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 8                 54 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 8                 54 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                11                 51 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                11                 51 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                 56 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                 56 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                13                 49 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                13                 49 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 56 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 56 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 59 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 59 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                12                 50 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                12                 50 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                20                 42 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                20                 42 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                 58 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                 58 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                12                 50 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                12                 50 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                11                 51 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                11                 51 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 8                 54 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 8                 54 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 6                 56 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 6                 56 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 56 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 56 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 8                 54 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 8                 54 
[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 62 columns.

Variable 1:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=6,	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=4,	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 62 columns, 0 survival variables, and 8 non-survival variables.
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=2, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=6, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               3                 9
  CLUS_3               1                19
  CLUS_4               2                12
D1V2, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               2                19
  CLUS_3               4                19
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2    4
  1P GAIN WILD-TYPE   18   16
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                18
  CLUS_2               4                16
D1V4, multiclass
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               5                17
  CLUS_2               1                22
  CLUS_3               2                15
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               2                22
  CLUS_3               4                20
D1V7, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3                11
  CLUS_2               1                 8
  CLUS_3               2                17
  CLUS_4               2                18
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               2                12
  CLUS_3               6                35

Clustering(2) Variable = 1q gain mutation analysis
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               6                10
  CLUS_2               5                 7
  CLUS_3               6                14
  CLUS_4              12                 2
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              11                 7
  CLUS_2               8                13
  CLUS_3              10                13
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     10    9
  1Q GAIN WILD-TYPE   10   11
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              10                10
  CLUS_2               9                11
D2V4, multiclass
D2V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              14                 8
  CLUS_2              10                13
  CLUS_3               5                12
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2              11                13
  CLUS_3              14                10
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               7                 7
  CLUS_2               4                 5
  CLUS_3               8                11
  CLUS_4              10                10
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3                 4
  CLUS_2               6                 8
  CLUS_3              20                21

Clustering(3) Variable = 2p gain mutation analysis
D3V1, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               4                12
  CLUS_2               2                10
  CLUS_3               1                19
  CLUS_4               3                11
D3V2, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               2                19
  CLUS_3               4                19
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2    3
  2P GAIN WILD-TYPE   18   17
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                18
  CLUS_2               3                17
D3V4, multiclass
D3V5, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               6                16
  CLUS_2               1                22
  CLUS_3               3                14
D3V6, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               2                22
  CLUS_3               6                18
D3V7, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               3                11
  CLUS_2               1                 8
  CLUS_3               3                16
  CLUS_4               3                17
D3V8, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               3                11
  CLUS_3               6                35

Clustering(4) Variable = 2q gain mutation analysis
D4V1, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               4                12
  CLUS_2               2                10
  CLUS_3               1                19
  CLUS_4               3                11
D4V2, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               2                19
  CLUS_3               4                19
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2    3
  2Q GAIN WILD-TYPE   18   17
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                18
  CLUS_2               3                17
D4V4, multiclass
D4V5, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               6                16
  CLUS_2               1                22
  CLUS_3               3                14
D4V6, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               2                22
  CLUS_3               6                18
D4V7, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               3                11
  CLUS_2               1                 8
  CLUS_3               3                16
  CLUS_4               3                17
D4V8, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               3                11
  CLUS_3               6                35

Clustering(5) Variable = 3p gain mutation analysis
D5V1, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               0                12
  CLUS_3               0                20
  CLUS_4               4                10
D5V2, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               1                20
  CLUS_3               2                21
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    4
  3P GAIN WILD-TYPE   20   16
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                20
  CLUS_2               4                16
D5V4, multiclass
D5V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4                18
  CLUS_2               0                23
  CLUS_3               2                15
D5V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               0                24
  CLUS_3               4                20
D5V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               1                 8
  CLUS_3               2                17
  CLUS_4               3                17
D5V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               0                14
  CLUS_3               5                36

Clustering(6) Variable = 3q gain mutation analysis
D6V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                13
  CLUS_2               1                11
  CLUS_3               0                20
  CLUS_4               3                11
D6V2, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               1                20
  CLUS_3               3                20
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0    4
  3Q GAIN WILD-TYPE   20   16
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                20
  CLUS_2               4                16
D6V4, multiclass
D6V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               5                17
  CLUS_2               1                22
  CLUS_3               1                16
D6V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               1                23
  CLUS_3               4                20
D6V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               2                 7
  CLUS_3               2                17
  CLUS_4               3                17
D6V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               0                14
  CLUS_3               5                36

Clustering(7) Variable = 4p gain mutation analysis
D7V1, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3                13
  CLUS_2               0                12
  CLUS_3               0                20
  CLUS_4               2                12
D7V2, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               0                21
  CLUS_3               4                19
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    2
  4P GAIN WILD-TYPE   19   18
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                19
  CLUS_2               2                18
D7V4, multiclass
D7V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                20
  CLUS_2               2                21
  CLUS_3               1                16
D7V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               2                22
  CLUS_3               1                23
D7V7, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               0                 9
  CLUS_3               1                18
  CLUS_4               4                16
D7V8, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               0                14
  CLUS_3               5                36

Clustering(8) Variable = 4q gain mutation analysis
D8V1, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3                13
  CLUS_2               0                12
  CLUS_3               0                20
  CLUS_4               2                12
D8V2, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               0                21
  CLUS_3               4                19
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    2
  4Q GAIN WILD-TYPE   19   18
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1                19
  CLUS_2               2                18
D8V4, multiclass
D8V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2                20
  CLUS_2               2                21
  CLUS_3               1                16
D8V6, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               2                22
  CLUS_3               1                23
D8V7, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               0                 9
  CLUS_3               1                18
  CLUS_4               4                16
D8V8, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               0                14
  CLUS_3               5                36

Clustering(9) Variable = 5p gain mutation analysis
D9V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                14
  CLUS_2               1                11
  CLUS_3               0                20
  CLUS_4               0                14
D9V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               0                21
  CLUS_3               2                21
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      0    0
  5P GAIN WILD-TYPE   20   20
D9V4, multiclass
D9V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                21
  CLUS_2               0                23
  CLUS_3               2                15
D9V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                23
  CLUS_3               1                23
D9V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               0                 9
  CLUS_3               1                18
  CLUS_4               1                19
D9V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               2                12
  CLUS_3               1                40

Clustering(10) Variable = 6p gain mutation analysis
D10V1, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               8                 8
  CLUS_2               4                 8
  CLUS_3               4                16
  CLUS_4              12                 2
D10V2, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              14                 4
  CLUS_2               3                18
  CLUS_3              11                12
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      8    8
  6P GAIN WILD-TYPE   12   12
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               8                12
  CLUS_2               8                12
D10V4, multiclass
D10V5, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              14                 8
  CLUS_2               9                14
  CLUS_3               5                12
D10V6, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2              10                14
  CLUS_3              14                10
D10V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               6                 8
  CLUS_2               1                 8
  CLUS_3               8                11
  CLUS_4              13                 7
D10V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               4                10
  CLUS_3              23                18

Clustering(11) Variable = 6q gain mutation analysis
D11V1, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                16
  CLUS_2               1                11
  CLUS_3               0                20
  CLUS_4               2                12
D11V2, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               0                21
  CLUS_3               1                22
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    2
  6Q GAIN WILD-TYPE   20   18
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                20
  CLUS_2               2                18
D11V4, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                38 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A1QB        TCGA-D3-A2J8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A2JO        TCGA-DA-A1HV        TCGA-EE-A17X        TCGA-EE-A184 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A20C        TCGA-EE-A29G        TCGA-EE-A29L 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GL 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2GP        TCGA-EE-A2GU        TCGA-EE-A2MC        TCGA-EE-A2MD 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2ML        TCGA-EE-A2MM        TCGA-EE-A2MN        TCGA-EE-A3AC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A195        TCGA-ER-A199        TCGA-ER-A19D        TCGA-ER-A19N 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A2NE        TCGA-ER-A2NH        TCGA-FS-A1YW        TCGA-FS-A1Z0 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z3        TCGA-FS-A1ZP        TCGA-FS-A1ZQ        TCGA-FS-A1ZT 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D11V5, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               2                20
  CLUS_2               1                22
  CLUS_3               0                17
D11V6, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               1                23
  CLUS_3               2                22
D11V7, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                14
  CLUS_2               0                 9
  CLUS_3               2                17
  CLUS_4               1                19
D11V8, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                13
  CLUS_3               2                39

Clustering(12) Variable = 7p gain mutation analysis
D12V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               6                10
  CLUS_2               1                11
  CLUS_3               0                20
  CLUS_4               4                10
D12V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                13
  CLUS_2               0                21
  CLUS_3               6                17
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4    1
  7P GAIN WILD-TYPE   16   19
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4                16
  CLUS_2               1                19
D12V4, multiclass
D12V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               7                15
  CLUS_2               3                20
  CLUS_3               1                16
D12V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               4                20
  CLUS_3               5                19
D12V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               4                10
  CLUS_2               0                 9
  CLUS_3               1                18
  CLUS_4               6                14
D12V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                13
  CLUS_3              10                31

Clustering(13) Variable = 7q gain mutation analysis
D13V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               7                 9
  CLUS_2               1                11
  CLUS_3               0                20
  CLUS_4               1                13
D13V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               1                20
  CLUS_3               4                19
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3    1
  7Q GAIN WILD-TYPE   17   19
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                17
  CLUS_2               1                19
D13V4, multiclass
D13V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               7                15
  CLUS_2               1                22
  CLUS_3               1                16
D13V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               2                22
  CLUS_3               5                19
D13V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                11
  CLUS_2               1                 8
  CLUS_3               1                18
  CLUS_4               4                16
D13V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               1                13
  CLUS_3               7                34

Clustering(14) Variable = 8p gain mutation analysis
D14V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               4                12
  CLUS_2               2                10
  CLUS_3               2                18
  CLUS_4               5                 9
D14V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               8                10
  CLUS_2               2                19
  CLUS_3               3                20
D14V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4    3
  8P GAIN WILD-TYPE   16   17
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               4                16
  CLUS_2               3                17
D14V4, multiclass
D14V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              11                11
  CLUS_2               2                21
  CLUS_3               0                17
D14V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               3                21
  CLUS_3               9                15
D14V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               1                 8
  CLUS_3               4                15
  CLUS_4               7                13
D14V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               3                11
  CLUS_3               9                32

Clustering(15) Variable = 8q gain mutation analysis
D15V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               6                10
  CLUS_2               2                10
  CLUS_3               4                16
  CLUS_4               9                 5
D15V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              12                 6
  CLUS_2               4                17
  CLUS_3               5                18
D15V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      8    4
  8Q GAIN WILD-TYPE   12   16
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               8                12
  CLUS_2               4                16
D15V4, multiclass
D15V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              15                 7
  CLUS_2               5                18
  CLUS_3               1                16
D15V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               6                18
  CLUS_3              13                11
D15V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               6                 8
  CLUS_2               2                 7
  CLUS_3               5                14
  CLUS_4               8                12
D15V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               4                10
  CLUS_3              15                26

Clustering(16) Variable = 9q gain mutation analysis
D16V1, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                15
  CLUS_2               2                10
  CLUS_3               0                20
  CLUS_4               1                13
D16V2, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               0                21
  CLUS_3               2                21
D16V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1    2
  9Q GAIN WILD-TYPE   19   18
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                19
  CLUS_2               2                18
D16V4, multiclass
D16V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                20
  CLUS_2               0                23
  CLUS_3               2                15
D16V6, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                12
  CLUS_2               0                24
  CLUS_3               2                22
D16V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                13
  CLUS_2               0                 9
  CLUS_3               2                17
  CLUS_4               1                19
D16V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               2                12
  CLUS_3               2                39

Clustering(17) Variable = 11p gain mutation analysis
D17V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                0                 12
  CLUS_3                2                 18
  CLUS_4                1                 13
D17V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                2                 19
  CLUS_3                1                 22
D17V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    1
  11P GAIN WILD-TYPE   19   19
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                1                 19
D17V4, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 38 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A1QB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2JO         TCGA-DA-A1HV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A184         TCGA-EE-A185 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20C         TCGA-EE-A29G         TCGA-EE-A29L 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29V 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GL         TCGA-EE-A2GU 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2MC         TCGA-EE-A2MD         TCGA-EE-A2ML 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2MM         TCGA-EE-A2MN         TCGA-EE-A3AC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A195         TCGA-ER-A199         TCGA-ER-A19D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A2NC         TCGA-ER-A2NE         TCGA-ER-A2NH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1YW         TCGA-FS-A1Z0         TCGA-FS-A1Z3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZQ         TCGA-FS-A1ZT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D17V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                1                 22
  CLUS_3                2                 15
D17V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 22
  CLUS_3                2                 22
D17V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                0                  9
  CLUS_3                3                 16
  CLUS_4                2                 18
D17V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                 13
  CLUS_3                4                 37

Clustering(18) Variable = 11q gain mutation analysis
D18V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                0                 12
  CLUS_3                2                 18
  CLUS_4                1                 13
D18V2, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                2                 19
  CLUS_3                1                 22
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    1
  11Q GAIN WILD-TYPE   19   19
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                1                 19
D18V4, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 38 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A1QB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2JO         TCGA-DA-A1HV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A184         TCGA-EE-A185 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20C         TCGA-EE-A29G         TCGA-EE-A29L 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29V 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GL         TCGA-EE-A2GU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2MC         TCGA-EE-A2MD         TCGA-EE-A2ML 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2MM         TCGA-EE-A2MN         TCGA-EE-A3AC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A195         TCGA-ER-A199         TCGA-ER-A19D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A2NC         TCGA-ER-A2NE         TCGA-ER-A2NH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1YW         TCGA-FS-A1Z0         TCGA-FS-A1Z3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZQ         TCGA-FS-A1ZT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D18V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                1                 22
  CLUS_3                2                 15
D18V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 22
  CLUS_3                2                 22
D18V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                0                  9
  CLUS_3                3                 16
  CLUS_4                2                 18
D18V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                 13
  CLUS_3                4                 37

Clustering(19) Variable = 12p gain mutation analysis
D19V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                0                 12
  CLUS_3                0                 20
  CLUS_4                1                 13
D19V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                 20
  CLUS_3                2                 21
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2    0
  12P GAIN WILD-TYPE   18   20
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                0                 20
D19V4, multiclass
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                 38 
        TCGA-D3-A1Q8         TCGA-D3-A1QB         TCGA-D3-A2J8 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2JO         TCGA-DA-A1HV         TCGA-EE-A17X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A184         TCGA-EE-A185         TCGA-EE-A20C 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29G         TCGA-EE-A29L         TCGA-EE-A29R 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A2A2 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2GL         TCGA-EE-A2GP         TCGA-EE-A2MC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2MD         TCGA-EE-A2ML         TCGA-EE-A2MM 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2MN         TCGA-EE-A3AC         TCGA-ER-A195 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A199         TCGA-ER-A19D         TCGA-ER-A19N 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A2NC         TCGA-ER-A2NE         TCGA-ER-A2NH 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1YW         TCGA-FS-A1Z0         TCGA-FS-A1Z3 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZQ         TCGA-FS-A1ZT 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
D19V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                0                 23
  CLUS_3                2                 15
D19V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                2                 22
  CLUS_3                2                 22
D19V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                  7
  CLUS_3                0                 19
  CLUS_4                1                 19
D19V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                0                 14
  CLUS_3                2                 39

Clustering(20) Variable = 13q gain mutation analysis
D20V1, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                7                  9
  CLUS_2                2                 10
  CLUS_3                2                 18
  CLUS_4                7                  7
D20V2, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               12                  6
  CLUS_2                2                 19
  CLUS_3                4                 19
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      6    4
  13Q GAIN WILD-TYPE   14   16
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                6                 14
  CLUS_2                4                 16
D20V4, multiclass
D20V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               13                  9
  CLUS_2                2                 21
  CLUS_3                3                 14
D20V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                3                 21
  CLUS_3               12                 12
D20V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                0                  9
  CLUS_3                6                 13
  CLUS_4                9                 11
D20V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                3                 11
  CLUS_3               15                 26

Clustering(21) Variable = 14q gain mutation analysis
D21V1, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                1                 11
  CLUS_3                1                 19
  CLUS_4                3                 11
D21V2, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 20
  CLUS_3                2                 21
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    1
  14Q GAIN WILD-TYPE   19   19
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                1                 19
D21V4, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                 38 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A1QB 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2JO         TCGA-DA-A1HV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A184         TCGA-EE-A185 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A20C         TCGA-EE-A29G         TCGA-EE-A29R 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A2A2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2GL         TCGA-EE-A2GP         TCGA-EE-A2GU 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2MC         TCGA-EE-A2MD         TCGA-EE-A2ML 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2MM         TCGA-EE-A2MN         TCGA-EE-A3AC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A195         TCGA-ER-A199         TCGA-ER-A19D 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A2NC         TCGA-ER-A2NE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A2NH         TCGA-FS-A1YW         TCGA-FS-A1Z0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1Z3         TCGA-FS-A1ZQ         TCGA-FS-A1ZT 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D21V5, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                3                 19
  CLUS_2                1                 22
  CLUS_3                1                 16
D21V6, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 23
  CLUS_3                3                 21
D21V7, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                  9
  CLUS_3                0                 19
  CLUS_4                4                 16
D21V8, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                 13
  CLUS_3                4                 37

Clustering(22) Variable = 15q gain mutation analysis
D22V1, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                2                 10
  CLUS_3                1                 19
  CLUS_4                2                 12
D22V2, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                2                 19
  CLUS_3                3                 20
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1    1
  15Q GAIN WILD-TYPE   19   19
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                1                 19
D22V4, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 38 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A1QB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2JO         TCGA-DA-A1HV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A184         TCGA-EE-A185 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A20C         TCGA-EE-A29G         TCGA-EE-A29L 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GL         TCGA-EE-A2GP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2GU         TCGA-EE-A2MC         TCGA-EE-A2MD 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2ML         TCGA-EE-A2MM         TCGA-EE-A3AC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A195         TCGA-ER-A199         TCGA-ER-A19D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A2NC         TCGA-ER-A2NE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A2NH         TCGA-FS-A1YW         TCGA-FS-A1Z0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZQ         TCGA-FS-A1ZT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D22V5, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                 18
  CLUS_2                2                 21
  CLUS_3                1                 16
D22V6, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                2                 22
  CLUS_3                5                 19
D22V7, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                1                  8
  CLUS_3                1                 18
  CLUS_4                3                 17
D22V8, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                2                 12
  CLUS_3                4                 37

Clustering(23) Variable = 16p gain mutation analysis
D23V1, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                 10
  CLUS_3                0                 20
  CLUS_4                4                 10
D23V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                5                 13
  CLUS_2                0                 21
  CLUS_3                2                 21
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1    1
  16P GAIN WILD-TYPE   19   19
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                1                 19
D23V4, multiclass
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                 38 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A1QB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2JO         TCGA-DA-A1HV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A184         TCGA-EE-A185 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A20C         TCGA-EE-A29G         TCGA-EE-A29L 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A2A2 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2GL         TCGA-EE-A2GP         TCGA-EE-A2GU 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2MC         TCGA-EE-A2MD         TCGA-EE-A2ML 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2MM         TCGA-EE-A2MN         TCGA-EE-A3AC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A195         TCGA-ER-A199         TCGA-ER-A19N 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A2NC         TCGA-ER-A2NE         TCGA-ER-A2NH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1YW         TCGA-FS-A1Z0         TCGA-FS-A1Z3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZQ         TCGA-FS-A1ZT 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
D23V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                7                 15
  CLUS_2                0                 23
  CLUS_3                0                 17
D23V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                 24
  CLUS_3                6                 18
D23V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                  9
  CLUS_3                3                 16
  CLUS_4                3                 17
D23V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                2                 12
  CLUS_3                5                 36

Clustering(24) Variable = 16q gain mutation analysis
D24V1, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                 10
  CLUS_3                0                 20
  CLUS_4                3                 11
D24V2, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                0                 21
  CLUS_3                2                 21
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    1
  16Q GAIN WILD-TYPE   19   19
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                1                 19
D24V4, multiclass
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 38 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A1QB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2JO         TCGA-DA-A1HV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A184         TCGA-EE-A185 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A20C         TCGA-EE-A29G         TCGA-EE-A29L 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A2A2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2GL         TCGA-EE-A2GP         TCGA-EE-A2GU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2MC         TCGA-EE-A2MD         TCGA-EE-A2ML 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2MM         TCGA-EE-A2MN         TCGA-EE-A3AC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A195         TCGA-ER-A199         TCGA-ER-A19N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A2NC         TCGA-ER-A2NE         TCGA-ER-A2NH 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1YW         TCGA-FS-A1Z0         TCGA-FS-A1Z3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZQ         TCGA-FS-A1ZT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
D24V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                6                 16
  CLUS_2                0                 23
  CLUS_3                0                 17
D24V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                 24
  CLUS_3                5                 19
D24V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                  9
  CLUS_3                2                 17
  CLUS_4                3                 17
D24V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                2                 12
  CLUS_3                4                 37

Clustering(25) Variable = 17p gain mutation analysis
D25V1, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                1                 11
  CLUS_3                0                 20
  CLUS_4                0                 14
D25V2, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                 20
  CLUS_3                1                 22
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1    0
  17P GAIN WILD-TYPE   19   20
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                0                 20
D25V4, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 39 
        TCGA-D3-A1Q8         TCGA-D3-A1QB         TCGA-D3-A2J8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2JO         TCGA-DA-A1HV         TCGA-EE-A17X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A184         TCGA-EE-A185         TCGA-EE-A20C 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29G         TCGA-EE-A29L         TCGA-EE-A29R 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A2A2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2GL         TCGA-EE-A2GP         TCGA-EE-A2GU 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2MC         TCGA-EE-A2MD         TCGA-EE-A2ML 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2MM         TCGA-EE-A2MN         TCGA-EE-A3AC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A195         TCGA-ER-A199         TCGA-ER-A19D 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A2NC         TCGA-ER-A2NE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A2NH         TCGA-FS-A1YW         TCGA-FS-A1Z0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1Z3         TCGA-FS-A1ZP         TCGA-FS-A1ZQ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZT         TCGA-GN-A267         TCGA-GN-A268 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D25V5, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                 19
  CLUS_2                0                 23
  CLUS_3                0                 17
D25V6, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                0                 24
  CLUS_3                3                 21
D25V7, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                1                  8
  CLUS_3                0                 19
  CLUS_4                0                 20
D25V8, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                 13
  CLUS_3                1                 40

Clustering(26) Variable = 17q gain mutation analysis
D26V1, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                2                 10
  CLUS_3                1                 19
  CLUS_4                2                 12
D26V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                 20
  CLUS_3                5                 18
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2    5
  17Q GAIN WILD-TYPE   18   15
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                5                 15
D26V4, multiclass
D26V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                4                 18
  CLUS_2                1                 22
  CLUS_3                4                 13
D26V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                1                 23
  CLUS_3                4                 20
D26V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                1                  8
  CLUS_3                1                 18
  CLUS_4                4                 16
D26V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                2                 12
  CLUS_3                6                 35

Clustering(27) Variable = 18p gain mutation analysis
D27V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                1                 11
  CLUS_3                0                 20
  CLUS_4                2                 12
D27V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                0                 21
  CLUS_3                3                 20
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    1
  18P GAIN WILD-TYPE   19   19
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                1                 19
D27V4, multiclass
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 38 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A1QB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2JO         TCGA-DA-A1HV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A184         TCGA-EE-A185 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A20C         TCGA-EE-A29G         TCGA-EE-A29R 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A2A2 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2GL         TCGA-EE-A2GP         TCGA-EE-A2GU 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2MC         TCGA-EE-A2MD         TCGA-EE-A2ML 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2MM         TCGA-EE-A2MN         TCGA-EE-A3AC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A195         TCGA-ER-A199         TCGA-ER-A19D 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A2NC         TCGA-ER-A2NE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A2NH         TCGA-FS-A1YW         TCGA-FS-A1Z0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1Z3         TCGA-FS-A1ZP         TCGA-FS-A1ZQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZT         TCGA-GN-A268 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
D27V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                1                 22
  CLUS_3                1                 16
D27V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 22
  CLUS_3                1                 23
D27V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                  9
  CLUS_3                0                 19
  CLUS_4                3                 17
D27V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                 13
  CLUS_3                3                 38

Clustering(28) Variable = 18q gain mutation analysis
D28V1, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                1                 11
  CLUS_3                0                 20
  CLUS_4                2                 12
D28V2, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                0                 21
  CLUS_3                3                 20
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    1
  18Q GAIN WILD-TYPE   19   19
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                1                 19
D28V4, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 38 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A1QB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2JO         TCGA-DA-A1HV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A184         TCGA-EE-A185 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20C         TCGA-EE-A29G         TCGA-EE-A29R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A2A2 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2GL         TCGA-EE-A2GP         TCGA-EE-A2GU 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2MC         TCGA-EE-A2MD         TCGA-EE-A2ML 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2MM         TCGA-EE-A2MN         TCGA-EE-A3AC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A195         TCGA-ER-A199         TCGA-ER-A19D 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A2NC         TCGA-ER-A2NE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A2NH         TCGA-FS-A1YW         TCGA-FS-A1Z0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1Z3         TCGA-FS-A1ZP         TCGA-FS-A1ZQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZT         TCGA-GN-A268 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D28V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                1                 22
  CLUS_3                1                 16
D28V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 22
  CLUS_3                1                 23
D28V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                  9
  CLUS_3                0                 19
  CLUS_4                3                 17
D28V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                 13
  CLUS_3                3                 38

Clustering(29) Variable = 19p gain mutation analysis
D29V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                2                 10
  CLUS_3                0                 20
  CLUS_4                3                 11
D29V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                0                 21
  CLUS_3                3                 20
D29V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    3
  19P GAIN WILD-TYPE   19   17
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                3                 17
D29V4, multiclass
D29V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                4                 18
  CLUS_2                0                 23
  CLUS_3                2                 15
D29V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 23
  CLUS_3                4                 20
D29V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                  9
  CLUS_3                1                 18
  CLUS_4                4                 16
D29V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                0                 14
  CLUS_3                6                 35

Clustering(30) Variable = 19q gain mutation analysis
D30V1, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                1                 11
  CLUS_3                1                 19
  CLUS_4                3                 11
D30V2, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                1                 20
  CLUS_3                2                 21
D30V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    3
  19Q GAIN WILD-TYPE   19   17
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                3                 17
D30V4, multiclass
D30V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                5                 17
  CLUS_2                0                 23
  CLUS_3                2                 15
D30V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 23
  CLUS_3                5                 19
D30V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                  9
  CLUS_3                2                 17
  CLUS_4                4                 16
D30V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                0                 14
  CLUS_3                7                 34

Clustering(31) Variable = 20p gain mutation analysis
D31V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                5                 11
  CLUS_2                2                 10
  CLUS_3                1                 19
  CLUS_4                5                  9
D31V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                7                 11
  CLUS_2                2                 19
  CLUS_3                4                 19
D31V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2    3
  20P GAIN WILD-TYPE   18   17
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                3                 17
D31V4, multiclass
D31V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               10                 12
  CLUS_2                1                 22
  CLUS_3                2                 15
D31V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 22
  CLUS_3               10                 14
D31V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                2                  7
  CLUS_3                5                 14
  CLUS_4                4                 16
D31V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                3                 11
  CLUS_3                8                 33

Clustering(32) Variable = 20q gain mutation analysis
D32V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                6                 10
  CLUS_2                2                 10
  CLUS_3                3                 17
  CLUS_4                7                  7
D32V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                8                 10
  CLUS_2                3                 18
  CLUS_3                7                 16
D32V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4    5
  20Q GAIN WILD-TYPE   16   15
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                4                 16
  CLUS_2                5                 15
D32V4, multiclass
D32V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               10                 12
  CLUS_2                4                 19
  CLUS_3                4                 13
D32V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                5                 19
  CLUS_3               10                 14
D32V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                2                  7
  CLUS_3                5                 14
  CLUS_4                8                 12
D32V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                3                 11
  CLUS_3               13                 28

Clustering(33) Variable = 21q gain mutation analysis
D33V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                2                 10
  CLUS_3                1                 19
  CLUS_4                4                 10
D33V2, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                2                 19
  CLUS_3                3                 20
D33V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1    2
  21Q GAIN WILD-TYPE   19   18
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                2                 18
D33V4, multiclass
D33V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                7                 15
  CLUS_2                1                 22
  CLUS_3                1                 16
D33V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                0                 24
  CLUS_3                7                 17
D33V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                  8
  CLUS_3                4                 15
  CLUS_4                3                 17
D33V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                3                 11
  CLUS_3                5                 36

Clustering(34) Variable = 22q gain mutation analysis
D34V1, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                5                 11
  CLUS_2                1                 11
  CLUS_3                0                 20
  CLUS_4                5                  9
D34V2, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                2                 19
  CLUS_3                5                 18
D34V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4    2
  22Q GAIN WILD-TYPE   16   18
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                4                 16
  CLUS_2                2                 18
D34V4, multiclass
D34V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                7                 15
  CLUS_2                3                 20
  CLUS_3                1                 16
D34V6, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                3                 21
  CLUS_3                6                 18
D34V7, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                1                  8
  CLUS_3                2                 17
  CLUS_4                6                 14
D34V8, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                 13
  CLUS_3                9                 32

Clustering(35) Variable = 2q loss mutation analysis
D35V1, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                16
  CLUS_2               1                11
  CLUS_3               2                18
  CLUS_4               0                14
D35V2, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               0                21
  CLUS_3               1                22
D35V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    0
  2Q LOSS WILD-TYPE   18   20
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                18
  CLUS_2               0                20
D35V4, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                38 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A1QB        TCGA-D3-A2J8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A2JO        TCGA-DA-A1HV        TCGA-EE-A17X        TCGA-EE-A184 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29G        TCGA-EE-A29L        TCGA-EE-A29R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2GP        TCGA-EE-A2GU        TCGA-EE-A2MC        TCGA-EE-A2MD 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2ML        TCGA-EE-A2MM        TCGA-EE-A2MN        TCGA-EE-A3AC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A195        TCGA-ER-A199        TCGA-ER-A19D        TCGA-ER-A19N 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A2NC        TCGA-ER-A2NE        TCGA-ER-A2NH        TCGA-FS-A1Z0 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z3        TCGA-FS-A1ZP        TCGA-FS-A1ZQ        TCGA-FS-A1ZT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D35V5, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                20
  CLUS_2               1                22
  CLUS_3               0                17
D35V6, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               0                24
  CLUS_3               3                21
D35V7, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               1                 8
  CLUS_3               0                19
  CLUS_4               2                18
D35V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                13
  CLUS_3               2                39

Clustering(36) Variable = 3p loss mutation analysis
D36V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                15
  CLUS_2               0                12
  CLUS_3               3                17
  CLUS_4               0                14
D36V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               2                19
  CLUS_3               1                22
D36V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1    2
  3P LOSS WILD-TYPE   19   18
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                19
  CLUS_2               2                18
D36V4, multiclass
D36V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                21
  CLUS_2               2                21
  CLUS_3               1                16
D36V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                22
  CLUS_3               1                23
D36V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                12
  CLUS_2               1                 8
  CLUS_3               1                18
  CLUS_4               0                20
D36V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               2                12
  CLUS_3               2                39

Clustering(37) Variable = 3q loss mutation analysis
D37V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                15
  CLUS_2               0                12
  CLUS_3               2                18
  CLUS_4               1                13
D37V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               1                20
  CLUS_3               3                20
D37V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    2
  3Q LOSS WILD-TYPE   19   18
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                19
  CLUS_2               2                18
D37V4, multiclass
D37V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                21
  CLUS_2               2                21
  CLUS_3               1                16
D37V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               2                22
  CLUS_3               1                23
D37V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               1                 8
  CLUS_3               1                18
  CLUS_4               2                18
D37V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               2                12
  CLUS_3               2                39

Clustering(38) Variable = 4p loss mutation analysis
D38V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               1                15
  CLUS_2               5                 7
  CLUS_3               2                18
  CLUS_4               1                13
D38V2, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               2                19
  CLUS_3               4                19
D38V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      6    1
  4P LOSS WILD-TYPE   14   19
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               6                14
  CLUS_2               1                19
D38V4, multiclass
D38V5, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               7                15
  CLUS_2               2                21
  CLUS_3               0                17
D38V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               2                22
  CLUS_3               7                17
D38V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               4                10
  CLUS_2               3                 6
  CLUS_3               2                17
  CLUS_4               0                20
D38V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               4                10
  CLUS_3               3                38

Clustering(39) Variable = 4q loss mutation analysis
D39V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                15
  CLUS_2               6                 6
  CLUS_3               2                18
  CLUS_4               1                13
D39V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               3                18
  CLUS_3               4                19
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      7    1
  4Q LOSS WILD-TYPE   13   19
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               7                13
  CLUS_2               1                19
D39V4, multiclass
D39V5, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               8                14
  CLUS_2               2                21
  CLUS_3               0                17
D39V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               2                22
  CLUS_3               8                16
D39V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               4                10
  CLUS_2               4                 5
  CLUS_3               2                17
  CLUS_4               0                20
D39V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               3                 4
  CLUS_2               4                10
  CLUS_3               3                38

Clustering(40) Variable = 5p loss mutation analysis
D40V1, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               5                11
  CLUS_2               3                 9
  CLUS_3               2                18
  CLUS_4               4                10
D40V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               3                18
  CLUS_3               9                14
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6    5
  5P LOSS WILD-TYPE   14   15
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               6                14
  CLUS_2               5                15
D40V4, multiclass
D40V5, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                19
  CLUS_2               6                17
  CLUS_3               5                12
D40V6, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               5                 9
  CLUS_2               5                19
  CLUS_3               4                20
D40V7, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               4                10
  CLUS_2               1                 8
  CLUS_3               2                17
  CLUS_4               7                13
D40V8, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               2                12
  CLUS_3              11                30

Clustering(41) Variable = 5q loss mutation analysis
D41V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               6                10
  CLUS_2               4                 8
  CLUS_3               3                17
  CLUS_4               2                12
D41V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               7                14
  CLUS_3               8                15
D41V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      6    6
  5Q LOSS WILD-TYPE   14   14
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               6                14
  CLUS_2               6                14
D41V4, multiclass
D41V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               2                20
  CLUS_2               6                17
  CLUS_3               7                10
D41V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               7                 7
  CLUS_2               5                19
  CLUS_3               3                21
D41V7, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               4                10
  CLUS_2               2                 7
  CLUS_3               4                15
  CLUS_4               5                15
D41V8, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               2                12
  CLUS_3              11                30

Clustering(42) Variable = 6p loss mutation analysis
D42V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                14
  CLUS_2               0                12
  CLUS_3               4                16
  CLUS_4               1                13
D42V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               5                16
  CLUS_3               2                21
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1    1
  6P LOSS WILD-TYPE   19   19
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                19
  CLUS_2               1                19
D42V4, multiclass
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2                38 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A1QB        TCGA-D3-A2J8 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A2JO        TCGA-DA-A1HV        TCGA-EE-A17X        TCGA-EE-A184 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A20C        TCGA-EE-A29G        TCGA-EE-A29L 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A2A2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2GL        TCGA-EE-A2GP        TCGA-EE-A2GU        TCGA-EE-A2MC 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2MD        TCGA-EE-A2ML        TCGA-EE-A2MM        TCGA-EE-A2MN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A3AC        TCGA-ER-A195        TCGA-ER-A199        TCGA-ER-A19D 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A2NC        TCGA-ER-A2NE        TCGA-ER-A2NH 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FS-A1YW        TCGA-FS-A1Z0        TCGA-FS-A1Z3        TCGA-FS-A1ZP 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
D42V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                22
  CLUS_2               3                20
  CLUS_3               4                13
D42V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3                11
  CLUS_2               1                23
  CLUS_3               3                21
D42V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                12
  CLUS_2               0                 9
  CLUS_3               4                15
  CLUS_4               1                19
D42V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               2                12
  CLUS_3               5                36

Clustering(43) Variable = 6q loss mutation analysis
D43V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              11                 5
  CLUS_2               1                11
  CLUS_3              12                 8
  CLUS_4               4                10
D43V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               7                11
  CLUS_2              11                10
  CLUS_3              10                13
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     12    6
  6Q LOSS WILD-TYPE    8   14
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              12                 8
  CLUS_2               6                14
D43V4, multiclass
D43V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6                16
  CLUS_2              12                11
  CLUS_3              10                 7
D43V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               8                 6
  CLUS_2              12                12
  CLUS_3               8                16
D43V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               8                 6
  CLUS_2               3                 6
  CLUS_3              11                 8
  CLUS_4               6                14
D43V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3                 4
  CLUS_2               5                 9
  CLUS_3              20                21

Clustering(44) Variable = 7p loss mutation analysis
D44V1, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                16
  CLUS_2               1                11
  CLUS_3               1                19
  CLUS_4               1                13
D44V2, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               0                21
  CLUS_3               1                22
D44V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1    0
  7P LOSS WILD-TYPE   19   20
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1                19
  CLUS_2               0                20
D44V4, multiclass
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                1                39 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A1QB        TCGA-D3-A2J8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D3-A2JO        TCGA-DA-A1HV        TCGA-EE-A17X        TCGA-EE-A184 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29G        TCGA-EE-A29L        TCGA-EE-A29R 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A2GP        TCGA-EE-A2GU        TCGA-EE-A2MC        TCGA-EE-A2MD 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A2ML        TCGA-EE-A2MM        TCGA-EE-A2MN        TCGA-EE-A3AC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A195        TCGA-ER-A199        TCGA-ER-A19D        TCGA-ER-A19N 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A2NC        TCGA-ER-A2NE        TCGA-ER-A2NH        TCGA-FS-A1YW 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FS-A1Z0        TCGA-FS-A1Z3        TCGA-FS-A1ZP        TCGA-FS-A1ZQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FS-A1ZT        TCGA-GN-A267        TCGA-GN-A268 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
D44V5, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               2                20
  CLUS_2               1                22
  CLUS_3               0                17
D44V6, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               0                24
  CLUS_3               3                21
D44V7, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                14
  CLUS_2               1                 8
  CLUS_3               1                18
  CLUS_4               1                19
D44V8, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                13
  CLUS_3               2                39

Clustering(45) Variable = 8p loss mutation analysis
D45V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               3                13
  CLUS_2               1                11
  CLUS_3               3                17
  CLUS_4               4                10
D45V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               5                13
  CLUS_2               2                19
  CLUS_3               4                19
D45V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      8    1
  8P LOSS WILD-TYPE   12   19
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               8                12
  CLUS_2               1                19
D45V4, multiclass
D45V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               5                17
  CLUS_2               4                19
  CLUS_3               2                15
D45V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               2                12
  CLUS_2               3                21
  CLUS_3               6                18
D45V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               7                 7
  CLUS_2               1                 8
  CLUS_3               3                16
  CLUS_4               0                20
D45V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                13
  CLUS_3              10                31

Clustering(46) Variable = 8q loss mutation analysis
D46V1, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                15
  CLUS_2               1                11
  CLUS_3               1                19
  CLUS_4               0                14
D46V2, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               0                21
  CLUS_3               3                20
D46V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    0
  8Q LOSS WILD-TYPE   17   20
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3                17
  CLUS_2               0                20
D46V4, multiclass
D46V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2                20
  CLUS_2               0                23
  CLUS_3               1                16
D46V6, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                13
  CLUS_2               0                24
  CLUS_3               2                22
D46V7, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2                12
  CLUS_2               1                 8
  CLUS_3               0                19
  CLUS_4               0                20
D46V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                13
  CLUS_3               2                39

Clustering(47) Variable = 9p loss mutation analysis
D47V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              12                 4
  CLUS_2               9                 3
  CLUS_3              10                10
  CLUS_4               7                 7
D47V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               9                 9
  CLUS_2              11                10
  CLUS_3              18                 5
D47V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      8   13
  9P LOSS WILD-TYPE   12    7
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               8                12
  CLUS_2              13                 7
D47V4, multiclass
D47V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              13                 9
  CLUS_2              12                11
  CLUS_3              13                 4
D47V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              10                 4
  CLUS_2              14                10
  CLUS_3              14                10
D47V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               8                 6
  CLUS_2               6                 3
  CLUS_3              10                 9
  CLUS_4              14                 6
D47V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               4                 3
  CLUS_2               7                 7
  CLUS_3              27                14

Clustering(48) Variable = 9q loss mutation analysis
D48V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               8                 8
  CLUS_2               7                 5
  CLUS_3              11                 9
  CLUS_4               4                10
D48V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               7                11
  CLUS_2               9                12
  CLUS_3              14                 9
D48V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      7    9
  9Q LOSS WILD-TYPE   13   11
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               7                13
  CLUS_2               9                11
D48V4, multiclass
D48V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              10                12
  CLUS_2              13                10
  CLUS_3               7                10
D48V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               5                 9
  CLUS_2              13                11
  CLUS_3              12                12
D48V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               5                 9
  CLUS_2               5                 4
  CLUS_3               8                11
  CLUS_4              12                 8
D48V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               4                 3
  CLUS_2               6                 8
  CLUS_3              20                21

Clustering(49) Variable = 10p loss mutation analysis
D49V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                9                  7
  CLUS_2                9                  3
  CLUS_3                0                 20
  CLUS_4                7                  7
D49V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               10                  8
  CLUS_2                3                 18
  CLUS_3               12                 11
D49V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      7    8
  10P LOSS WILD-TYPE   13   12
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                7                 13
  CLUS_2                8                 12
D49V4, multiclass
D49V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               13                  9
  CLUS_2                4                 19
  CLUS_3                8                  9
D49V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                  8
  CLUS_2                6                 18
  CLUS_3               13                 11
D49V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                  8
  CLUS_2                3                  6
  CLUS_3                5                 14
  CLUS_4               11                  9
D49V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                3                  4
  CLUS_2                4                 10
  CLUS_3               18                 23

Clustering(50) Variable = 10q loss mutation analysis
D50V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                8                  8
  CLUS_2               10                  2
  CLUS_3                2                 18
  CLUS_4                7                  7
D50V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               11                  7
  CLUS_2                5                 16
  CLUS_3               11                 12
D50V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      7    8
  10Q LOSS WILD-TYPE   13   12
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                7                 13
  CLUS_2                8                 12
D50V4, multiclass
D50V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               14                  8
  CLUS_2                5                 18
  CLUS_3                8                  9
D50V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                  9
  CLUS_2                8                 16
  CLUS_3               14                 10
D50V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                7                  7
  CLUS_2                4                  5
  CLUS_3                6                 13
  CLUS_4               10                 10
D50V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                3                  4
  CLUS_2                4                 10
  CLUS_3               20                 21

Clustering(51) Variable = 11p loss mutation analysis
D51V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                 10
  CLUS_2                4                  8
  CLUS_3                4                 16
  CLUS_4                5                  9
D51V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                 12
  CLUS_2                2                 19
  CLUS_3               11                 12
D51V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      8    4
  11P LOSS WILD-TYPE   12   16
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                8                 12
  CLUS_2                4                 16
D51V4, multiclass
D51V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                9                 13
  CLUS_2                5                 18
  CLUS_3                5                 12
D51V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                6                 18
  CLUS_3                9                 15
D51V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                5                  9
  CLUS_2                3                  6
  CLUS_3                5                 14
  CLUS_4                6                 14
D51V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                4                 10
  CLUS_3               13                 28

Clustering(52) Variable = 11q loss mutation analysis
D52V1, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                6                 10
  CLUS_2                5                  7
  CLUS_3                6                 14
  CLUS_4                5                  9
D52V2, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                7                 11
  CLUS_2                5                 16
  CLUS_3               10                 13
D52V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      8    6
  11Q LOSS WILD-TYPE   12   14
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                8                 12
  CLUS_2                6                 14
D52V4, multiclass
D52V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                9                 13
  CLUS_2                8                 15
  CLUS_3                5                 12
D52V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                4                 10
  CLUS_2               10                 14
  CLUS_3                8                 16
D52V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                5                  9
  CLUS_2                4                  5
  CLUS_3                6                 13
  CLUS_4                7                 13
D52V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                3                  4
  CLUS_2                6                  8
  CLUS_3               13                 28

Clustering(53) Variable = 12p loss mutation analysis
D53V1, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                1                 11
  CLUS_3                3                 17
  CLUS_4                1                 13
D53V2, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 20
  CLUS_3                5                 18
D53V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    2
  12P LOSS WILD-TYPE   17   18
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                3                 17
  CLUS_2                2                 18
D53V4, multiclass
D53V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                4                 19
  CLUS_3                2                 15
D53V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                4                 20
  CLUS_3                3                 21
D53V7, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                  7
  CLUS_3                2                 17
  CLUS_4                3                 17
D53V8, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                2                 12
  CLUS_3                5                 36

Clustering(54) Variable = 12q loss mutation analysis
D54V1, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                5                 11
  CLUS_2                1                 11
  CLUS_3                3                 17
  CLUS_4                2                 12
D54V2, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                1                 20
  CLUS_3                6                 17
D54V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      4    2
  12Q LOSS WILD-TYPE   16   18
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                4                 16
  CLUS_2                2                 18
D54V4, multiclass
D54V5, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                4                 18
  CLUS_2                4                 19
  CLUS_3                3                 14
D54V6, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                4                 20
  CLUS_3                5                 19
D54V7, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                2                  7
  CLUS_3                3                 16
  CLUS_4                3                 17
D54V8, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                2                 12
  CLUS_3                8                 33

Clustering(55) Variable = 13q loss mutation analysis
D55V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                1                 11
  CLUS_3                2                 18
  CLUS_4                2                 12
D55V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                2                 19
  CLUS_3                4                 19
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    1
  13Q LOSS WILD-TYPE   18   19
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                1                 19
D55V4, multiclass
D55V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 21
  CLUS_2                3                 20
  CLUS_3                2                 15
D55V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                3                 21
  CLUS_3                2                 22
D55V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                 14
  CLUS_2                1                  8
  CLUS_3                1                 18
  CLUS_4                4                 16
D55V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                 13
  CLUS_3                4                 37

Clustering(56) Variable = 14q loss mutation analysis
D56V1, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                8                  8
  CLUS_2                2                 10
  CLUS_3                0                 20
  CLUS_4                3                 11
D56V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                6                 12
  CLUS_2                2                 19
  CLUS_3                5                 18
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4    4
  14Q LOSS WILD-TYPE   16   16
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                4                 16
  CLUS_2                4                 16
D56V4, multiclass
D56V5, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                4                 18
  CLUS_2                4                 19
  CLUS_3                5                 12
D56V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                5                 19
  CLUS_3                4                 20
D56V7, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                1                  8
  CLUS_3                3                 16
  CLUS_4                5                 15
D56V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                 13
  CLUS_3               12                 29

Clustering(57) Variable = 15q loss mutation analysis
D57V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 16
  CLUS_2                1                 11
  CLUS_3                1                 19
  CLUS_4                4                 10
D57V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                0                 21
  CLUS_3                2                 21
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    1
  15Q LOSS WILD-TYPE   19   19
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                1                 19
D57V4, multiclass
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 38 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A1QB 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2JO         TCGA-DA-A1HV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A184         TCGA-EE-A185 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20C         TCGA-EE-A29G         TCGA-EE-A29R 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A2A2 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2GL         TCGA-EE-A2GP         TCGA-EE-A2GU 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2MC         TCGA-EE-A2MD         TCGA-EE-A2ML 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2MM         TCGA-EE-A2MN         TCGA-EE-A3AC 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A195         TCGA-ER-A199         TCGA-ER-A19D 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A2NC         TCGA-ER-A2NE 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A2NH         TCGA-FS-A1YW         TCGA-FS-A1Z3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZQ         TCGA-FS-A1ZT 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
D57V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                3                 20
  CLUS_3                1                 16
D57V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                 22
  CLUS_3                3                 21
D57V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                0                  9
  CLUS_3                1                 18
  CLUS_4                3                 17
D57V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                0                 14
  CLUS_3                6                 35

Clustering(58) Variable = 16p loss mutation analysis
D58V1, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                1                 11
  CLUS_3                0                 20
  CLUS_4                0                 14
D58V2, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                0                 21
  CLUS_3                2                 21
D58V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    0
  16P LOSS WILD-TYPE   20   20
D58V4, multiclass
D58V5, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 22
  CLUS_2                1                 22
  CLUS_3                2                 15
D58V6, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 23
  CLUS_3                1                 23
D58V7, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                  9
  CLUS_3                0                 19
  CLUS_4                2                 18
D58V8, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                0                 14
  CLUS_3                3                 38

Clustering(59) Variable = 16q loss mutation analysis
D59V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                 11
  CLUS_2                2                 10
  CLUS_3                3                 17
  CLUS_4                2                 12
D59V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                 13
  CLUS_2                3                 18
  CLUS_3                4                 19
D59V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    3
  16Q LOSS WILD-TYPE   17   17
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                 17
  CLUS_2                3                 17
D59V4, multiclass
D59V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                 17
  CLUS_2                2                 21
  CLUS_3                5                 12
D59V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                4                 20
  CLUS_3                5                 19
D59V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                  7
  CLUS_3                3                 16
  CLUS_4                6                 14
D59V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                 13
  CLUS_3               11                 30

Clustering(60) Variable = 17p loss mutation analysis
D60V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                8                  8
  CLUS_2                2                 10
  CLUS_3                5                 15
  CLUS_4                5                  9
D60V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                6                 15
  CLUS_3               10                 13
D60V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4    8
  17P LOSS WILD-TYPE   16   12
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                 16
  CLUS_2                8                 12
D60V4, multiclass
D60V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                6                 16
  CLUS_2                7                 16
  CLUS_3                7                 10
D60V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                6                  8
  CLUS_2                7                 17
  CLUS_3                7                 17
D60V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                4                  5
  CLUS_3                7                 12
  CLUS_4                5                 15
D60V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                3                 11
  CLUS_3               15                 26

Clustering(61) Variable = 17q loss mutation analysis
D61V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                1                 11
  CLUS_3                0                 20
  CLUS_4                0                 14
D61V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                 20
  CLUS_3                2                 21
D61V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0    2
  17Q LOSS WILD-TYPE   20   18
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 20
  CLUS_2                2                 18
D61V4, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 38 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A1QB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2JO         TCGA-DA-A1HV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A184         TCGA-EE-A185 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20C         TCGA-EE-A29G         TCGA-EE-A29L 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29V 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GL         TCGA-EE-A2GU 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2MC         TCGA-EE-A2MD         TCGA-EE-A2ML 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2MM         TCGA-EE-A2MN         TCGA-EE-A3AC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A195         TCGA-ER-A199         TCGA-ER-A19D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A2NC         TCGA-ER-A2NE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A2NH         TCGA-FS-A1YW         TCGA-FS-A1Z0 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1Z3         TCGA-FS-A1ZP         TCGA-FS-A1ZT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
D61V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                0                 23
  CLUS_3                2                 15
D61V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                0                 24
  CLUS_3                2                 22
D61V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                1                  8
  CLUS_3                1                 18
  CLUS_4                0                 20
D61V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                0                 14
  CLUS_3                3                 38

Clustering(62) Variable = 18p loss mutation analysis
D62V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                6                 10
  CLUS_2                3                  9
  CLUS_3                2                 18
  CLUS_4                1                 13
D62V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                3                 18
  CLUS_3                5                 18
D62V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    3
  18P LOSS WILD-TYPE   16   17
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                4                 16
  CLUS_2                3                 17
D62V4, multiclass
D62V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                6                 16
  CLUS_2                3                 20
  CLUS_3                3                 14
D62V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                2                 22
  CLUS_3                7                 17
D62V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                2                  7
  CLUS_3                2                 17
  CLUS_4                4                 16
D62V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                 13
  CLUS_3               10                 31

Clustering(63) Variable = 18q loss mutation analysis
D63V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                6                 10
  CLUS_2                2                 10
  CLUS_3                2                 18
  CLUS_4                1                 13
D63V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                3                 18
  CLUS_3                4                 19
D63V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    3
  18Q LOSS WILD-TYPE   17   17
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                 17
  CLUS_2                3                 17
D63V4, multiclass
D63V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                5                 17
  CLUS_2                3                 20
  CLUS_3                3                 14
D63V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                2                 22
  CLUS_3                6                 18
D63V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                 11
  CLUS_2                2                  7
  CLUS_3                2                 17
  CLUS_4                4                 16
D63V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                 13
  CLUS_3                9                 32

Clustering(64) Variable = 19p loss mutation analysis
D64V1, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                 12
  CLUS_2                3                  9
  CLUS_3                1                 19
  CLUS_4                0                 14
D64V2, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                3                 18
  CLUS_3                3                 20
D64V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    2
  19P LOSS WILD-TYPE   18   18
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 18
  CLUS_2                2                 18
D64V4, multiclass
D64V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                4                 19
  CLUS_3                2                 15
D64V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                3                 21
  CLUS_3                3                 21
D64V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                 10
  CLUS_2                0                  9
  CLUS_3                1                 18
  CLUS_4                3                 17
D64V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                2                 12
  CLUS_3                6                 35

Clustering(65) Variable = 19q loss mutation analysis
D65V1, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                3                 13
  CLUS_2                2                 10
  CLUS_3                1                 19
  CLUS_4                0                 14
D65V2, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                2                 19
  CLUS_3                3                 20
D65V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    2
  19Q LOSS WILD-TYPE   19   18
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 19
  CLUS_2                2                 18
D65V4, multiclass
D65V5, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 22
  CLUS_2                5                 18
  CLUS_3                1                 16
D65V6, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                4                 20
  CLUS_3                1                 23
D65V7, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                0                  9
  CLUS_3                2                 17
  CLUS_4                3                 17
D65V8, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                 13
  CLUS_3                5                 36

Clustering(66) Variable = 21q loss mutation analysis
D66V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 14
  CLUS_2                1                 11
  CLUS_3                2                 18
  CLUS_4                1                 13
D66V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 20
  CLUS_3                3                 20
D66V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    1
  21Q LOSS WILD-TYPE   17   19
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 17
  CLUS_2                1                 19
D66V4, multiclass
D66V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                 22
  CLUS_2                4                 19
  CLUS_3                2                 15
D66V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 12
  CLUS_2                3                 21
  CLUS_3                1                 23
D66V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                2                  7
  CLUS_3                1                 18
  CLUS_4                2                 18
D66V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                1                 13
  CLUS_3                3                 38

Clustering(67) Variable = 22q loss mutation analysis
D67V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                 15
  CLUS_2                4                  8
  CLUS_3                2                 18
  CLUS_4                1                 13
D67V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                2                 19
  CLUS_3                2                 21
D67V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4    2
  22Q LOSS WILD-TYPE   16   18
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                4                 16
  CLUS_2                2                 18
D67V4, multiclass
D67V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                5                 17
  CLUS_2                2                 21
  CLUS_3                1                 16
D67V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                 23
  CLUS_3                6                 18
D67V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                 13
  CLUS_2                1                  8
  CLUS_3                2                 17
  CLUS_4                4                 16
D67V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                 13
  CLUS_3                6                 35
                     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")
