
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/347747/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/KIRP-TP/2709428/1.GDAC_mergedClustering.Finished/KIRP-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KIRP-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=KIRP-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=117, in cluster file=117, common to both=117
[1] "Reduce the number of clustering variables from 80 to 59."
[1]  59 117
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8               109 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8               109 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               11               106 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               11               106 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13               104 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13               104 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               28                89 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               28                89 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               32                85 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               32                85 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               113 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               113 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               114 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               114 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               106 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               11               106 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               11               106 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               11               106 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4               113 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4               113 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3               114 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3               114 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               64                53 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               64                53 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               65                52 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               65                52 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7               110 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7               110 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                9               108 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                9               108 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                113 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                113 
[1] "10q gain mutation analysis"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                114 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                114 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                36                 81 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                36                 81 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                36                 81 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                36                 81 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                14                103 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                14                103 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                54                 63 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                54                 63 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                51                 66 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                51                 66 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                61                 56 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                61                 56 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                71                 46 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                71                 46 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                111 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                111 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                113 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                113 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                37                 80 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                37                 80 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                38                 79 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                38                 79 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                113 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                113 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4               113 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4               113 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               12               105 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               12               105 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                7               110 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                7               110 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                7               110 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                7               110 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3               114 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3               114 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10               107 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10               107 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10               107 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10               107 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                5               112 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                5               112 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                5               112 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                5               112 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                9               108 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                9               108 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               11               106 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               11               106 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3               114 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3               114 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               14               103 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               14               103 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               14               103 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               14               103 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                111 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                111 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 7                110 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 7                110 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 8                109 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 8                109 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                10                107 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                10                107 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                10                107 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                10                107 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                20                 97 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                20                 97 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                10                107 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                10                107 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 3                114 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 3                114 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                112 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                112 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                17                100 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                17                100 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                18                 99 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                18                 99 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                113 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                113 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                114 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                114 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                12                105 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                12                105 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                21                 96 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                21                 96 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               114 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               114 
[1] "data2feature, selection=ALL"
[1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
[4] "METHLYATION_CNMF"      "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 8 rows and 117 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
[4] "METHLYATION_CNMF"      "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 117 columns, 0 survival variables, and 8 non-survival variables.
MRNA_CNMF, nv=2, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1q gain mutation analysis
D1V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1    0
  1Q GAIN WILD-TYPE    6    9
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               0                 9
D1V2, multiclass
[1] "Remove cluster labels:" "1Q GAIN MUTATED"       
clus
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                1                15 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
D1V3, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               2                22
  CLUS_2               1                19
  CLUS_3               4                24
  CLUS_4               1                44
D1V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                21
  CLUS_2               7                20
  CLUS_3               0                39
D1V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               0                27
  CLUS_2               6                18
  CLUS_3               1                24
D1V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               0                37
  CLUS_3               4                17
D1V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               4                34
  CLUS_3               1                34
  CLUS_4               2                15
D1V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3                24
  CLUS_2               5                40
  CLUS_3               0                12
  CLUS_4               0                33

Clustering(2) Variable = 2p gain mutation analysis
D2V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2    1
  2P GAIN WILD-TYPE    5    8
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               1                 8
D2V2, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               2                 5
  CLUS_3               1                 4
D2V3, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               6                18
  CLUS_2               2                18
  CLUS_3               3                25
  CLUS_4               0                45
D2V4, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               0                21
  CLUS_2               2                25
  CLUS_3               6                33
D2V5, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               5                22
  CLUS_2               3                21
  CLUS_3               2                23
D2V6, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               7                30
  CLUS_3               1                20
D2V7, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                25
  CLUS_2               3                35
  CLUS_3               4                31
  CLUS_4               2                15
D2V8, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               2                43
  CLUS_3               3                 9
  CLUS_4               5                28

Clustering(3) Variable = 2q gain mutation analysis
D3V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2    1
  2Q GAIN WILD-TYPE    5    8
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               1                 8
D3V2, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               2                 5
  CLUS_3               1                 4
D3V3, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               6                18
  CLUS_2               2                18
  CLUS_3               5                23
  CLUS_4               0                45
D3V4, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                20
  CLUS_2               2                25
  CLUS_3               7                32
D3V5, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               6                21
  CLUS_2               3                21
  CLUS_3               2                23
D3V6, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               8                29
  CLUS_3               1                20
D3V7, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                25
  CLUS_2               4                34
  CLUS_3               5                30
  CLUS_4               2                15
D3V8, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               4                41
  CLUS_3               3                 9
  CLUS_4               5                28

Clustering(4) Variable = 3p gain mutation analysis
D4V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4    2
  3P GAIN WILD-TYPE    3    7
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4                 3
  CLUS_2               2                 7
D4V2, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               2                 5
  CLUS_3               4                 1
D4V3, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              21                 3
  CLUS_2               2                18
  CLUS_3               0                28
  CLUS_4               5                40
D4V4, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                18
  CLUS_2               2                25
  CLUS_3              13                26
D4V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1              12                15
  CLUS_2               0                24
  CLUS_3               7                18
D4V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                18
  CLUS_2              19                18
  CLUS_3               0                21
D4V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               7                20
  CLUS_2               5                33
  CLUS_3              14                21
  CLUS_4               2                15
D4V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               6                39
  CLUS_3               8                 4
  CLUS_4              13                20

Clustering(5) Variable = 3q gain mutation analysis
D5V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4    2
  3Q GAIN WILD-TYPE    3    7
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               4                 3
  CLUS_2               2                 7
D5V2, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               2                 5
  CLUS_3               4                 1
D5V3, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              20                 4
  CLUS_2               4                16
  CLUS_3               2                26
  CLUS_4               6                39
D5V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                18
  CLUS_2               3                24
  CLUS_3              15                24
D5V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              14                13
  CLUS_2               0                24
  CLUS_3               8                17
D5V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2              20                17
  CLUS_3               1                20
D5V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1              10                17
  CLUS_2               5                33
  CLUS_3              15                20
  CLUS_4               2                15
D5V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               4                23
  CLUS_2               6                39
  CLUS_3               8                 4
  CLUS_4              14                19

Clustering(6) Variable = 4p gain mutation analysis
D6V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    0
  4P GAIN WILD-TYPE    5    9
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               0                 9
D6V2, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                14 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4115        TCGA-B9-4116 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D6V3, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                24
  CLUS_2               1                19
  CLUS_3               2                26
  CLUS_4               1                44
D6V4, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                85 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7584        TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-7915        TCGA-A4-7996        TCGA-A4-7997 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B9-5155 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-5156        TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7773 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GL-7966        TCGA-HE-7128        TCGA-HE-7129        TCGA-HE-7130 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-J7-6720 
"4P GAIN WILD-TYPE" 
D6V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                25
  CLUS_2               2                22
  CLUS_3               0                25
D6V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               2                35
  CLUS_3               1                20
D6V7, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                27
  CLUS_2               2                36
  CLUS_3               1                34
  CLUS_4               1                16
D6V8, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               1                44
  CLUS_3               0                12
  CLUS_4               2                31

Clustering(7) Variable = 4q gain mutation analysis
D7V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    0
  4Q GAIN WILD-TYPE    6    9
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               0                 9
D7V2, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4115 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D7V3, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                24
  CLUS_2               1                19
  CLUS_3               1                27
  CLUS_4               1                44
D7V4, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                85 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7584        TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-7915        TCGA-A4-7996        TCGA-A4-7997 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B9-5155 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-5156        TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7773 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GL-7966        TCGA-HE-7128        TCGA-HE-7129        TCGA-HE-7130 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-J7-6720 
"4Q GAIN WILD-TYPE" 
D7V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2                25
  CLUS_2               1                23
  CLUS_3               0                25
D7V6, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               2                35
  CLUS_3               0                21
D7V7, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                27
  CLUS_2               1                37
  CLUS_3               1                34
  CLUS_4               1                16
D7V8, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               0                27
  CLUS_2               1                44
  CLUS_3               0                12
  CLUS_4               2                31

Clustering(8) Variable = 5p gain mutation analysis
D8V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    0
  5P GAIN WILD-TYPE    5    9
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               0                 9
D8V2, multiclass
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                14 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4617 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
D8V3, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                21
  CLUS_2               1                19
  CLUS_3               5                23
  CLUS_4               2                43
D8V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                19
  CLUS_2               4                23
  CLUS_3               1                38
D8V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                25
  CLUS_2               5                19
  CLUS_3               1                24
D8V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               3                34
  CLUS_3               3                18
D8V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                25
  CLUS_2               3                35
  CLUS_3               3                32
  CLUS_4               3                14
D8V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4                23
  CLUS_2               3                42
  CLUS_3               1                11
  CLUS_4               3                30

Clustering(9) Variable = 5q gain mutation analysis
D9V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    0
  5Q GAIN WILD-TYPE    5    9
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                 5
  CLUS_2               0                 9
D9V2, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                14 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4617 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D9V3, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                21
  CLUS_2               1                19
  CLUS_3               5                23
  CLUS_4               2                43
D9V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                19
  CLUS_2               4                23
  CLUS_3               1                38
D9V5, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                25
  CLUS_2               4                20
  CLUS_3               2                23
D9V6, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               3                34
  CLUS_3               3                18
D9V7, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                24
  CLUS_2               3                35
  CLUS_3               3                32
  CLUS_4               2                15
D9V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               5                22
  CLUS_2               3                42
  CLUS_3               0                12
  CLUS_4               3                30

Clustering(10) Variable = 6p gain mutation analysis
D10V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1    0
  6P GAIN WILD-TYPE    6    9
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               0                 9
D10V2, multiclass
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                15 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D10V3, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               0                24
  CLUS_2               1                19
  CLUS_3               2                26
  CLUS_4               1                44
D10V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               0                21
  CLUS_2               2                25
  CLUS_3               1                38
D10V5, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               3                21
  CLUS_3               0                25
D10V6, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               1                36
  CLUS_3               2                19
D10V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               0                27
  CLUS_2               3                35
  CLUS_3               0                35
  CLUS_4               1                16
D10V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               2                43
  CLUS_3               1                11
  CLUS_4               0                33

Clustering(11) Variable = 6q gain mutation analysis
D11V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    0
  6Q GAIN WILD-TYPE    6    9
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               0                 9
D11V2, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                15 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D11V3, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                24
  CLUS_2               1                19
  CLUS_3               2                26
  CLUS_4               0                45
D11V4, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                85 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7584        TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-7915        TCGA-A4-7996        TCGA-A4-7997 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B9-5155 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-5156        TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7773 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GL-7966        TCGA-HE-7128        TCGA-HE-7129        TCGA-HE-7130 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-J7-6720 
"6Q GAIN WILD-TYPE" 
D11V5, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               2                22
  CLUS_3               0                25
D11V6, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               1                36
  CLUS_3               1                20
D11V7, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                27
  CLUS_2               2                36
  CLUS_3               0                35
  CLUS_4               1                16
D11V8, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               1                44
  CLUS_3               1                11
  CLUS_4               0                33

Clustering(12) Variable = 7p gain mutation analysis
D12V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5    5
  7P GAIN WILD-TYPE    2    4
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                 2
  CLUS_2               5                 4
D12V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               3                 1
  CLUS_2               3                 4
  CLUS_3               4                 1
D12V3, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              20                 4
  CLUS_2              20                 0
  CLUS_3               6                22
  CLUS_4              18                27
D12V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              11                10
  CLUS_2               6                21
  CLUS_3              28                11
D12V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              22                 5
  CLUS_2               5                19
  CLUS_3              12                13
D12V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               5                13
  CLUS_2              29                 8
  CLUS_3               5                16
D12V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              11                16
  CLUS_2              19                19
  CLUS_3              27                 8
  CLUS_4               7                10
D12V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              10                17
  CLUS_2              21                24
  CLUS_3              10                 2
  CLUS_4              23                10

Clustering(13) Variable = 7q gain mutation analysis
D13V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5    5
  7Q GAIN WILD-TYPE    2    4
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               5                 2
  CLUS_2               5                 4
D13V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                 1
  CLUS_2               3                 4
  CLUS_3               4                 1
D13V3, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              21                 3
  CLUS_2              20                 0
  CLUS_3               6                22
  CLUS_4              18                27
D13V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              11                10
  CLUS_2               7                20
  CLUS_3              28                11
D13V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              22                 5
  CLUS_2               6                18
  CLUS_3              12                13
D13V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               6                12
  CLUS_2              29                 8
  CLUS_3               5                16
D13V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              11                16
  CLUS_2              19                19
  CLUS_3              28                 7
  CLUS_4               7                10
D13V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              10                17
  CLUS_2              22                23
  CLUS_3              10                 2
  CLUS_4              23                10

Clustering(14) Variable = 8p gain mutation analysis
D14V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0    1
  8P GAIN WILD-TYPE    7    8
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                 8
D14V2, multiclass
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3472 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D14V3, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               2                22
  CLUS_2               0                20
  CLUS_3               2                26
  CLUS_4               3                42
D14V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                20
  CLUS_2               3                24
  CLUS_3               0                39
D14V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               2                22
  CLUS_3               2                23
D14V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               1                36
  CLUS_3               3                18
D14V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               4                34
  CLUS_3               2                33
  CLUS_4               0                17
D14V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               4                41
  CLUS_3               0                12
  CLUS_4               2                31

Clustering(15) Variable = 8q gain mutation analysis
D15V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1    1
  8Q GAIN WILD-TYPE    6    8
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               1                 8
D15V2, multiclass
[1] "Remove cluster labels:" "8Q GAIN MUTATED"       
clus
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                14 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3472        TCGA-AL-3473 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
D15V3, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                22
  CLUS_2               0                20
  CLUS_3               4                24
  CLUS_4               3                42
D15V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                20
  CLUS_2               4                23
  CLUS_3               0                39
D15V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               4                20
  CLUS_3               2                23
D15V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               1                36
  CLUS_3               4                17
D15V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               6                32
  CLUS_3               2                33
  CLUS_4               0                17
D15V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                25
  CLUS_2               5                40
  CLUS_3               0                12
  CLUS_4               2                31

Clustering(16) Variable = 10p gain mutation analysis
D16V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    1
  10P GAIN WILD-TYPE    6    8
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                  8
D16V2, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 14 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3471 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B3-3925 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
D16V3, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                2                 22
  CLUS_2                1                 19
  CLUS_3                1                 27
  CLUS_4                0                 45
D16V4, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 86 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7584         TCGA-A4-7585 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7732         TCGA-A4-7734         TCGA-A4-7828 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-7996         TCGA-A4-7997 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-5398         TCGA-B1-7332 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-7966         TCGA-HE-7128 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HE-7129         TCGA-J7-6720 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
D16V5, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                1                 23
  CLUS_3                0                 25
D16V6, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                2                 35
  CLUS_3                0                 21
D16V7, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                0                 38
  CLUS_3                3                 32
  CLUS_4                0                 17
D16V8, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                1                 44
  CLUS_3                0                 12
  CLUS_4                2                 31

Clustering(17) Variable = 10q gain mutation analysis
D17V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    1
  10Q GAIN WILD-TYPE    6    8
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                  8
D17V2, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 14 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3471 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B3-3925 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D17V3, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 23
  CLUS_2                1                 19
  CLUS_3                1                 27
  CLUS_4                0                 45
D17V4, multiclass
D17V5, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 74 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-5156         TCGA-BQ-5876 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7056 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DZ-6131         TCGA-DZ-6132 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-HE-7128 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HE-7129         TCGA-HE-7130 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D17V6, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 74 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-5156         TCGA-BQ-5876 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7056 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DZ-6131         TCGA-DZ-6132 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-HE-7128 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HE-7129         TCGA-HE-7130 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D17V7, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                0                 38
  CLUS_3                2                 33
  CLUS_4                0                 17
D17V8, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                0                 45
  CLUS_3                0                 12
  CLUS_4                2                 31

Clustering(18) Variable = 12p gain mutation analysis
D18V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3    3
  12P GAIN WILD-TYPE    4    6
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                  4
  CLUS_2                3                  6
D18V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                1                  6
  CLUS_3                4                  1
D18V3, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                9                 15
  CLUS_2               11                  9
  CLUS_3                7                 21
  CLUS_4                9                 36
D18V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                9                 12
  CLUS_2                6                 21
  CLUS_3               10                 29
D18V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               12                 15
  CLUS_2                5                 19
  CLUS_3                6                 19
D18V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2               16                 21
  CLUS_3                4                 17
D18V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               12                 15
  CLUS_2                7                 31
  CLUS_3               12                 23
  CLUS_4                5                 12
D18V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1               11                 16
  CLUS_2                8                 37
  CLUS_3                4                  8
  CLUS_4               13                 20

Clustering(19) Variable = 12q gain mutation analysis
D19V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3    3
  12Q GAIN WILD-TYPE    4    6
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                  4
  CLUS_2                3                  6
D19V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                  3
  CLUS_2                1                  6
  CLUS_3                4                  1
D19V3, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                9                 15
  CLUS_2               11                  9
  CLUS_3                7                 21
  CLUS_4                9                 36
D19V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                9                 12
  CLUS_2                6                 21
  CLUS_3               10                 29
D19V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               12                 15
  CLUS_2                5                 19
  CLUS_3                6                 19
D19V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2               16                 21
  CLUS_3                4                 17
D19V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               12                 15
  CLUS_2                7                 31
  CLUS_3               12                 23
  CLUS_4                5                 12
D19V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1               11                 16
  CLUS_2                8                 37
  CLUS_3                4                  8
  CLUS_4               13                 20

Clustering(20) Variable = 13q gain mutation analysis
D20V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1    1
  13Q GAIN WILD-TYPE    6    8
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                  8
D20V2, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 14 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B3-4104         TCGA-B9-4113         TCGA-B9-4114 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D20V3, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                7                 17
  CLUS_2                2                 18
  CLUS_3                1                 27
  CLUS_4                4                 41
D20V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                 18
  CLUS_2                1                 26
  CLUS_3                4                 35
D20V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                5                 22
  CLUS_2                1                 23
  CLUS_3                4                 21
D20V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                8                 29
  CLUS_3                0                 21
D20V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                 24
  CLUS_2                4                 34
  CLUS_3                6                 29
  CLUS_4                1                 16
D20V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                5                 40
  CLUS_3                4                  8
  CLUS_4                4                 29

Clustering(21) Variable = 16p gain mutation analysis
D21V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5    2
  16P GAIN WILD-TYPE    2    7
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                5                  2
  CLUS_2                2                  7
D21V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                3                  4
  CLUS_3                4                  1
D21V3, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               20                  4
  CLUS_2                8                 12
  CLUS_3                7                 21
  CLUS_4               19                 26
D21V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                8                 13
  CLUS_2                9                 18
  CLUS_3               20                 19
D21V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               15                 12
  CLUS_2                4                 20
  CLUS_3               13                 12
D21V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2               24                 13
  CLUS_3                6                 15
D21V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               14                 13
  CLUS_2               12                 26
  CLUS_3               24                 11
  CLUS_4                4                 13
D21V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1               11                 16
  CLUS_2               12                 33
  CLUS_3                8                  4
  CLUS_4               23                 10

Clustering(22) Variable = 16q gain mutation analysis
D22V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4    2
  16Q GAIN WILD-TYPE    3    7
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                  3
  CLUS_2                2                  7
D22V2, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                2                  5
  CLUS_3                4                  1
D22V3, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               20                  4
  CLUS_2                8                 12
  CLUS_3                5                 23
  CLUS_4               18                 27
D22V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                8                 13
  CLUS_2                7                 20
  CLUS_3               20                 19
D22V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               15                 12
  CLUS_2                3                 21
  CLUS_3               11                 14
D22V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2               24                 13
  CLUS_3                3                 18
D22V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1               12                 15
  CLUS_2               11                 27
  CLUS_3               24                 11
  CLUS_4                4                 13
D22V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                8                 19
  CLUS_2               12                 33
  CLUS_3                8                  4
  CLUS_4               23                 10

Clustering(23) Variable = 17p gain mutation analysis
D23V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5    5
  17P GAIN WILD-TYPE    2    4
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                5                  2
  CLUS_2                5                  4
D23V2, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                  1
  CLUS_2                3                  4
  CLUS_3                4                  1
D23V3, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1               22                  2
  CLUS_2               20                  0
  CLUS_3                3                 25
  CLUS_4               16                 29
D23V4, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                8                 13
  CLUS_2                5                 22
  CLUS_3               28                 11
D23V5, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1               20                  7
  CLUS_2                3                 21
  CLUS_3               10                 15
D23V6, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2               27                 10
  CLUS_3                3                 18
D23V7, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1               13                 14
  CLUS_2               17                 21
  CLUS_3               24                 11
  CLUS_4                7                 10
D23V8, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                8                 19
  CLUS_2               20                 25
  CLUS_3                9                  3
  CLUS_4               24                  9

Clustering(24) Variable = 17q gain mutation analysis
D24V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6    5
  17Q GAIN WILD-TYPE    1    4
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                6                  1
  CLUS_2                5                  4
D24V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                  1
  CLUS_2                4                  3
  CLUS_3                4                  1
D24V3, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               22                  2
  CLUS_2               20                  0
  CLUS_3                8                 20
  CLUS_4               21                 24
D24V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                9                 12
  CLUS_2               12                 15
  CLUS_3               29                 10
D24V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               20                  7
  CLUS_2                8                 16
  CLUS_3               13                 12
D24V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                6                 12
  CLUS_2               28                  9
  CLUS_3                7                 14
D24V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               16                 11
  CLUS_2               22                 16
  CLUS_3               25                 10
  CLUS_4                8                  9
D24V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1               13                 14
  CLUS_2               25                 20
  CLUS_3                9                  3
  CLUS_4               24                  9

Clustering(25) Variable = 18p gain mutation analysis
D25V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    1
  18P GAIN WILD-TYPE    5    8
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                1                  8
D25V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                3                  4
  CLUS_3                0                  5
D25V3, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                4                 20
  CLUS_2                0                 20
  CLUS_3                1                 27
  CLUS_4                1                 44
D25V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 21
  CLUS_2                0                 27
  CLUS_3                3                 36
D25V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                2                 22
  CLUS_3                1                 24
D25V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                3                 34
  CLUS_3                1                 20
D25V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                3                 35
  CLUS_3                2                 33
  CLUS_4                0                 17
D25V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                2                 43
  CLUS_3                1                 11
  CLUS_4                2                 31

Clustering(26) Variable = 18q gain mutation analysis
D26V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    0
  18Q GAIN WILD-TYPE    6    9
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                0                  9
D26V2, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 15 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4104 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D26V3, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                4                 20
  CLUS_2                0                 20
  CLUS_3                0                 28
  CLUS_4                0                 45
D26V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 21
  CLUS_2                0                 27
  CLUS_3                3                 36
D26V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                0                 24
  CLUS_3                1                 24
D26V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                3                 34
  CLUS_3                0                 21
D26V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                1                 37
  CLUS_3                2                 33
  CLUS_4                0                 17
D26V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                1                 44
  CLUS_3                1                 11
  CLUS_4                2                 31

Clustering(27) Variable = 20p gain mutation analysis
D27V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5    2
  20P GAIN WILD-TYPE    2    7
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                5                  2
  CLUS_2                2                  7
D27V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                4                  3
  CLUS_3                3                  2
D27V3, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               13                 11
  CLUS_2               10                 10
  CLUS_3                6                 22
  CLUS_4                8                 37
D27V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                5                 16
  CLUS_2                4                 23
  CLUS_3               15                 24
D27V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               15                 12
  CLUS_2                6                 18
  CLUS_3                2                 23
D27V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2               17                 20
  CLUS_3                3                 18
D27V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                8                 19
  CLUS_2               11                 27
  CLUS_3               15                 20
  CLUS_4                3                 14
D27V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                7                 20
  CLUS_2               10                 35
  CLUS_3                5                  7
  CLUS_4               15                 18

Clustering(28) Variable = 20q gain mutation analysis
D28V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5    3
  20Q GAIN WILD-TYPE    2    6
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                5                  2
  CLUS_2                3                  6
D28V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                5                  2
  CLUS_3                3                  2
D28V3, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               13                 11
  CLUS_2               10                 10
  CLUS_3                6                 22
  CLUS_4                9                 36
D28V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                5                 16
  CLUS_2                5                 22
  CLUS_3               14                 25
D28V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               15                 12
  CLUS_2                8                 16
  CLUS_3                2                 23
D28V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                5                 13
  CLUS_2               17                 20
  CLUS_3                3                 18
D28V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                7                 20
  CLUS_2               12                 26
  CLUS_3               16                 19
  CLUS_4                3                 14
D28V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                7                 20
  CLUS_2               12                 33
  CLUS_3                5                  7
  CLUS_4               14                 19

Clustering(29) Variable = 21q gain mutation analysis
D29V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1    0
  21Q GAIN WILD-TYPE    6    9
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                0                  9
D29V2, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 15 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B3-4104         TCGA-B9-4113         TCGA-B9-4114 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4617 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D29V3, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                2                 22
  CLUS_2                1                 19
  CLUS_3                0                 28
  CLUS_4                1                 44
D29V4, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 86 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7828         TCGA-A4-7915 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-7996         TCGA-A4-7997         TCGA-AL-7173 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B9-5155 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-B9-7268         TCGA-BQ-5875 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DZ-6131 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7773 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GL-7966         TCGA-HE-7128         TCGA-HE-7129 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-HE-7130         TCGA-J7-6720 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D29V5, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 75 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-B3-3925 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4617         TCGA-B9-5156 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-HE-7128         TCGA-HE-7129         TCGA-HE-7130 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D29V6, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 75 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-B3-3925 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4617         TCGA-B9-5156 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-HE-7128         TCGA-HE-7129         TCGA-HE-7130 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D29V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                0                 38
  CLUS_3                3                 32
  CLUS_4                1                 16
D29V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                0                 45
  CLUS_3                1                 11
  CLUS_4                3                 30

Clustering(30) Variable = Xq gain mutation analysis
D30V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    1
  XQ GAIN WILD-TYPE    7    8
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                 8
D30V2, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D30V3, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                23
  CLUS_2               2                18
  CLUS_3               1                27
  CLUS_4               0                45
D30V4, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                21
  CLUS_2               2                25
  CLUS_3               1                38
D30V5, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               2                25
  CLUS_2               2                22
  CLUS_3               0                25
D30V6, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               2                35
  CLUS_3               1                20
D30V7, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               0                27
  CLUS_2               1                37
  CLUS_3               2                33
  CLUS_4               1                16
D30V8, multiclass
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               1                44
  CLUS_3               0                12
  CLUS_4               2                31

Clustering(31) Variable = 1p loss mutation analysis
D31V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0    1
  1P LOSS WILD-TYPE    7    8
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                 8
D31V2, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D31V3, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2                22
  CLUS_2               0                20
  CLUS_3               6                22
  CLUS_4               4                41
D31V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2                19
  CLUS_2               3                24
  CLUS_3               4                35
D31V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3                24
  CLUS_2               1                23
  CLUS_3               1                24
D31V6, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               3                34
  CLUS_3               2                19
D31V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               4                23
  CLUS_2               0                38
  CLUS_3               7                28
  CLUS_4               1                16
D31V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3                24
  CLUS_2               2                43
  CLUS_3               0                12
  CLUS_4               7                26

Clustering(32) Variable = 1q loss mutation analysis
D32V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    1
  1Q LOSS WILD-TYPE    7    8
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                 8
D32V2, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
D32V3, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2                22
  CLUS_2               0                20
  CLUS_3               4                24
  CLUS_4               1                44
D32V4, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               1                20
  CLUS_2               0                27
  CLUS_3               4                35
D32V5, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               3                24
  CLUS_2               0                24
  CLUS_3               0                25
D32V6, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               3                34
  CLUS_3               0                21
D32V7, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               2                25
  CLUS_2               0                38
  CLUS_3               5                30
  CLUS_4               0                17
D32V8, multiclass
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               1                44
  CLUS_3               0                12
  CLUS_4               6                27

Clustering(33) Variable = 3p loss mutation analysis
D33V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1    0
  3P LOSS WILD-TYPE    6    9
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               0                 9
D33V2, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
D33V3, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                24
  CLUS_2               0                20
  CLUS_3               6                22
  CLUS_4               1                44
D33V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                21
  CLUS_2               5                22
  CLUS_3               0                39
D33V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               4                20
  CLUS_3               2                23
D33V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               0                37
  CLUS_3               4                17
D33V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                25
  CLUS_2               2                36
  CLUS_3               0                35
  CLUS_4               3                14
D33V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               3                24
  CLUS_2               3                42
  CLUS_3               1                11
  CLUS_4               0                33

Clustering(34) Variable = 3q loss mutation analysis
D34V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    0
  3Q LOSS WILD-TYPE    7    9
D34V2, multiclass
D34V3, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                24
  CLUS_2               0                20
  CLUS_3               3                25
  CLUS_4               0                45
D34V4, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                21
  CLUS_2               3                24
  CLUS_3               0                39
D34V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               3                21
  CLUS_3               0                25
D34V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               0                37
  CLUS_3               1                20
D34V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               1                37
  CLUS_3               0                35
  CLUS_4               1                16
D34V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               2                43
  CLUS_3               0                12
  CLUS_4               0                33

Clustering(35) Variable = 4p loss mutation analysis
D35V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      0    1
  4P LOSS WILD-TYPE    7    8
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                 8
D35V2, multiclass
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D35V3, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               3                21
  CLUS_2               0                20
  CLUS_3               5                23
  CLUS_4               2                43
D35V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                21
  CLUS_2               7                20
  CLUS_3               1                38
D35V5, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               6                18
  CLUS_3               0                25
D35V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               1                36
  CLUS_3               3                18
D35V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                25
  CLUS_2               4                34
  CLUS_3               2                33
  CLUS_4               2                15
D35V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               2                25
  CLUS_2               5                40
  CLUS_3               1                11
  CLUS_4               2                31

Clustering(36) Variable = 4q loss mutation analysis
D36V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      0    1
  4Q LOSS WILD-TYPE    7    8
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                 8
D36V2, multiclass
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
D36V3, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               3                21
  CLUS_2               0                20
  CLUS_3               6                22
  CLUS_4               1                44
D36V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                21
  CLUS_2               7                20
  CLUS_3               1                38
D36V5, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               5                19
  CLUS_3               1                24
D36V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               1                36
  CLUS_3               4                17
D36V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               2                25
  CLUS_2               4                34
  CLUS_3               2                33
  CLUS_4               2                15
D36V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               2                25
  CLUS_2               4                41
  CLUS_3               2                10
  CLUS_4               2                31

Clustering(37) Variable = 5p loss mutation analysis
D37V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0    0
  5P LOSS WILD-TYPE    7    9
D37V2, multiclass
D37V3, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                23
  CLUS_2               0                20
  CLUS_3               3                25
  CLUS_4               1                44
D37V4, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                20
  CLUS_2               3                24
  CLUS_3               1                38
D37V5, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               3                21
  CLUS_3               0                25
D37V6, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               1                36
  CLUS_3               0                21
D37V7, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2                25
  CLUS_2               3                35
  CLUS_3               0                35
  CLUS_4               0                17
D37V8, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               3                42
  CLUS_3               0                12
  CLUS_4               1                32

Clustering(38) Variable = 5q loss mutation analysis
D38V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0    0
  5Q LOSS WILD-TYPE    7    9
D38V2, multiclass
D38V3, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               2                22
  CLUS_2               0                20
  CLUS_3               2                26
  CLUS_4               1                44
D38V4, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                20
  CLUS_2               3                24
  CLUS_3               1                38
D38V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               2                22
  CLUS_3               0                25
D38V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               1                36
  CLUS_3               0                21
D38V7, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               2                25
  CLUS_2               3                35
  CLUS_3               0                35
  CLUS_4               0                17
D38V8, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               3                42
  CLUS_3               0                12
  CLUS_4               1                32

Clustering(39) Variable = 6p loss mutation analysis
D39V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    1
  6P LOSS WILD-TYPE    7    8
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                 8
D39V2, multiclass
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
D39V3, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                22
  CLUS_2               0                20
  CLUS_3               5                23
  CLUS_4               2                43
D39V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                20
  CLUS_2               4                23
  CLUS_3               3                36
D39V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               4                23
  CLUS_2               3                21
  CLUS_3               1                24
D39V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               4                33
  CLUS_3               2                19
D39V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                25
  CLUS_2               2                36
  CLUS_3               5                30
  CLUS_4               0                17
D39V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               4                41
  CLUS_3               0                12
  CLUS_4               4                29

Clustering(40) Variable = 6q loss mutation analysis
D40V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0    1
  6Q LOSS WILD-TYPE    7    8
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                 8
D40V2, multiclass
[1] "Remove cluster labels:" "6Q LOSS MUTATED"       
clus
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
D40V3, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                22
  CLUS_2               0                20
  CLUS_3               6                22
  CLUS_4               3                42
D40V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                19
  CLUS_2               5                22
  CLUS_3               2                37
D40V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3                24
  CLUS_2               4                20
  CLUS_3               1                24
D40V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               3                34
  CLUS_3               2                19
D40V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                25
  CLUS_2               3                35
  CLUS_3               5                30
  CLUS_4               1                16
D40V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               2                25
  CLUS_2               6                39
  CLUS_3               0                12
  CLUS_4               3                30

Clustering(41) Variable = 8p loss mutation analysis
D41V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0    1
  8P LOSS WILD-TYPE    7    8
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                 8
D41V2, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
D41V3, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               2                22
  CLUS_2               0                20
  CLUS_3               1                27
  CLUS_4               0                45
D41V4, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                85 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7584        TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-7915        TCGA-A4-7996        TCGA-A4-7997 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B9-5155        TCGA-B9-5156 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7773 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GL-7966        TCGA-HE-7128        TCGA-HE-7129        TCGA-HE-7130 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-J7-6720 
"8P LOSS WILD-TYPE" 
D41V5, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                74 
       TCGA-A4-7997        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B3-3925        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5156        TCGA-BQ-5876        TCGA-BQ-5877 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5561 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966        TCGA-HE-7128 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-HE-7129        TCGA-HE-7130 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
D41V6, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                74 
       TCGA-A4-7997        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B3-3925        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5156        TCGA-BQ-5876        TCGA-BQ-5877 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5561 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966        TCGA-HE-7128 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-HE-7129        TCGA-HE-7130 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
D41V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               1                37
  CLUS_3               1                34
  CLUS_4               0                17
D41V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               1                44
  CLUS_3               0                12
  CLUS_4               2                31

Clustering(42) Variable = 9p loss mutation analysis
D42V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1    2
  9P LOSS WILD-TYPE    6    7
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               2                 7
D42V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               0                 4
  CLUS_2               2                 5
  CLUS_3               1                 4
D42V3, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               3                21
  CLUS_2               0                20
  CLUS_3               8                20
  CLUS_4               3                42
D42V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               3                18
  CLUS_2               7                20
  CLUS_3               0                39
D42V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               8                16
  CLUS_3               2                23
D42V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               5                13
  CLUS_2               2                35
  CLUS_3               4                17
D42V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               7                31
  CLUS_3               3                32
  CLUS_4               3                14
D42V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               2                25
  CLUS_2               8                37
  CLUS_3               1                11
  CLUS_4               3                30

Clustering(43) Variable = 9q loss mutation analysis
D43V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1    1
  9Q LOSS WILD-TYPE    6    8
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                 6
  CLUS_2               1                 8
D43V2, multiclass
[1] "Remove cluster labels:" "9Q LOSS MUTATED"       
clus
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                14 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103        TCGA-B3-4104 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
D43V3, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               3                21
  CLUS_2               0                20
  CLUS_3               7                21
  CLUS_4               4                41
D43V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               4                17
  CLUS_2               7                20
  CLUS_3               0                39
D43V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               7                17
  CLUS_3               2                23
D43V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               4                14
  CLUS_2               2                35
  CLUS_3               4                17
D43V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               7                31
  CLUS_3               4                31
  CLUS_4               2                15
D43V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               2                25
  CLUS_2               9                36
  CLUS_3               1                11
  CLUS_4               2                31

Clustering(44) Variable = 10p loss mutation analysis
D44V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    1
  10P LOSS WILD-TYPE    6    8
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                  8
D44V2, multiclass
[1] "Remove cluster labels:" "10P LOSS MUTATED"      
clus
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 2                 14 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B3-3925 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
D44V3, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                 24
  CLUS_2                0                 20
  CLUS_3                6                 22
  CLUS_4                0                 45
D44V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                 21
  CLUS_2                3                 24
  CLUS_3                1                 38
D44V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                4                 20
  CLUS_3                1                 24
D44V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 36
  CLUS_3                3                 18
D44V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                3                 35
  CLUS_3                1                 34
  CLUS_4                2                 15
D44V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                2                 43
  CLUS_3                1                 11
  CLUS_4                1                 32

Clustering(45) Variable = 10q loss mutation analysis
D45V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1    0
  10Q LOSS WILD-TYPE    6    9
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                0                  9
D45V2, multiclass
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 1                 15 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B3-3925 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
D45V3, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                 24
  CLUS_2                0                 20
  CLUS_3                6                 22
  CLUS_4                1                 44
D45V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                 21
  CLUS_2                4                 23
  CLUS_3                1                 38
D45V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                4                 20
  CLUS_3                1                 24
D45V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                 36
  CLUS_3                4                 17
D45V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                4                 34
  CLUS_3                1                 34
  CLUS_4                1                 16
D45V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                3                 24
  CLUS_2                3                 42
  CLUS_3                1                 11
  CLUS_4                0                 33

Clustering(46) Variable = 11p loss mutation analysis
D46V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0    1
  11P LOSS WILD-TYPE    7    8
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                  8
D46V2, multiclass
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                 15 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D46V3, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                3                 21
  CLUS_2                0                 20
  CLUS_3                4                 24
  CLUS_4                1                 44
D46V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                 21
  CLUS_2                5                 22
  CLUS_3                2                 37
D46V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                4                 20
  CLUS_3                1                 24
D46V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                 36
  CLUS_3                2                 19
D46V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                3                 35
  CLUS_3                2                 33
  CLUS_4                1                 16
D46V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                5                 40
  CLUS_3                1                 11
  CLUS_4                1                 32

Clustering(47) Variable = 11q loss mutation analysis
D47V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    0
  11Q LOSS WILD-TYPE    7    9
D47V2, multiclass
D47V3, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 22
  CLUS_2                0                 20
  CLUS_3                6                 22
  CLUS_4                2                 43
D47V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                 21
  CLUS_2                7                 20
  CLUS_3                2                 37
D47V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                4                 20
  CLUS_3                3                 22
D47V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                 36
  CLUS_3                4                 17
D47V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                3                 24
  CLUS_2                3                 35
  CLUS_3                3                 32
  CLUS_4                1                 16
D47V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                5                 40
  CLUS_3                1                 11
  CLUS_4                2                 31

Clustering(48) Variable = 13q loss mutation analysis
D48V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0    1
  13Q LOSS WILD-TYPE    7    8
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                  8
D48V2, multiclass
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                 15 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-4103         TCGA-B3-4104 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D48V3, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 23
  CLUS_2                0                 20
  CLUS_3                5                 23
  CLUS_4                4                 41
D48V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                 21
  CLUS_2                7                 20
  CLUS_3                1                 38
D48V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                4                 20
  CLUS_3                0                 25
D48V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                2                 35
  CLUS_3                1                 20
D48V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                6                 32
  CLUS_3                2                 33
  CLUS_4                1                 16
D48V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                7                 38
  CLUS_3                0                 12
  CLUS_4                1                 32

Clustering(49) Variable = 14q loss mutation analysis
D49V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2    2
  14Q LOSS WILD-TYPE    5    7
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                2                  7
D49V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                3                  4
  CLUS_3                1                  4
D49V3, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                3                 21
  CLUS_2                0                 20
  CLUS_3               17                 11
  CLUS_4                0                 45
D49V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                5                 16
  CLUS_2                5                 22
  CLUS_3                4                 35
D49V5, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                7                 17
  CLUS_3                4                 21
D49V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                3                 34
  CLUS_3                6                 15
D49V7, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                3                 24
  CLUS_2                7                 31
  CLUS_3                5                 30
  CLUS_4                5                 12
D49V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                5                 22
  CLUS_2                7                 38
  CLUS_3                2                 10
  CLUS_4                6                 27

Clustering(50) Variable = 15q loss mutation analysis
D50V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0    1
  15Q LOSS WILD-TYPE    7    8
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                  8
D50V2, multiclass
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                 15 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-4103         TCGA-B3-4104 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
D50V3, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                 22
  CLUS_2                0                 20
  CLUS_3                6                 22
  CLUS_4                2                 43
D50V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                3                 18
  CLUS_2                4                 23
  CLUS_3                2                 37
D50V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                4                 20
  CLUS_3                2                 23
D50V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                4                 33
  CLUS_3                1                 20
D50V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                3                 24
  CLUS_2                3                 35
  CLUS_3                4                 31
  CLUS_4                0                 17
D50V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                5                 40
  CLUS_3                0                 12
  CLUS_4                3                 30

Clustering(51) Variable = 16q loss mutation analysis
D51V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0    0
  16Q LOSS WILD-TYPE    7    9
D51V2, multiclass
D51V3, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 22
  CLUS_2                0                 20
  CLUS_3                1                 27
  CLUS_4                0                 45
D51V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 21
  CLUS_2                3                 24
  CLUS_3                0                 39
D51V5, multiclass
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 74 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-B3-3925 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5876         TCGA-BQ-5877 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7056         TCGA-BQ-7058 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6795 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HE-7128         TCGA-HE-7129 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D51V6, multiclass
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 74 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-B3-3925 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5876         TCGA-BQ-5877 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7056         TCGA-BQ-7058 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6795 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HE-7128         TCGA-HE-7129 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D51V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                2                 36
  CLUS_3                1                 34
  CLUS_4                0                 17
D51V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                3                 42
  CLUS_3                0                 12
  CLUS_4                0                 33

Clustering(52) Variable = 17p loss mutation analysis
D52V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1    0
  17P LOSS WILD-TYPE    6    9
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                0                  9
D52V2, multiclass
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                 15 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B3-3925 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
D52V3, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 22
  CLUS_2                0                 20
  CLUS_3                2                 26
  CLUS_4                1                 44
D52V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                 21
  CLUS_2                4                 23
  CLUS_3                0                 39
D52V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                3                 21
  CLUS_3                0                 25
D52V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                0                 37
  CLUS_3                1                 20
D52V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                4                 34
  CLUS_3                1                 34
  CLUS_4                0                 17
D52V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                4                 41
  CLUS_3                0                 12
  CLUS_4                0                 33

Clustering(53) Variable = 18p loss mutation analysis
D53V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0    1
  18P LOSS WILD-TYPE    7    8
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                  8
D53V2, multiclass
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                 15 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B3-4104         TCGA-B9-4113         TCGA-B9-4114 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4117         TCGA-B9-4617 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
D53V3, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 21
  CLUS_2                2                 18
  CLUS_3                4                 24
  CLUS_4                8                 37
D53V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 18
  CLUS_2                8                 19
  CLUS_3                3                 36
D53V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                6                 18
  CLUS_3                3                 22
D53V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                5                 13
  CLUS_2                1                 36
  CLUS_3                4                 17
D53V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                7                 20
  CLUS_2                6                 32
  CLUS_3                2                 33
  CLUS_4                2                 15
D53V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                5                 22
  CLUS_2                8                 37
  CLUS_3                0                 12
  CLUS_4                4                 29

Clustering(54) Variable = 18q loss mutation analysis
D54V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      0    1
  18Q LOSS WILD-TYPE    7    8
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                  7
  CLUS_2                1                  8
D54V2, multiclass
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                 15 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B3-4104         TCGA-B9-4113         TCGA-B9-4114 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4117         TCGA-B9-4617 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
D54V3, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                4                 20
  CLUS_2                2                 18
  CLUS_3                4                 24
  CLUS_4                8                 37
D54V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                3                 18
  CLUS_2                9                 18
  CLUS_3                3                 36
D54V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                7                 17
  CLUS_3                3                 22
D54V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                6                 12
  CLUS_2                1                 36
  CLUS_3                4                 17
D54V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                7                 20
  CLUS_2                6                 32
  CLUS_3                3                 32
  CLUS_4                2                 15
D54V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                5                 22
  CLUS_2                9                 36
  CLUS_3                0                 12
  CLUS_4                4                 29

Clustering(55) Variable = 19p loss mutation analysis
D55V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    0
  19P LOSS WILD-TYPE    7    9
D55V2, multiclass
D55V3, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 22
  CLUS_2                0                 20
  CLUS_3                2                 26
  CLUS_4                0                 45
D55V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                 20
  CLUS_2                1                 26
  CLUS_3                2                 37
D55V5, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 74 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-B3-3925 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5877         TCGA-BQ-5878 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-HE-7128 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-HE-7129         TCGA-HE-7130 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D55V6, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 74 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-B3-3925 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5877         TCGA-BQ-5878 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-HE-7128 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-HE-7129         TCGA-HE-7130 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D55V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                1                 37
  CLUS_3                1                 34
  CLUS_4                0                 17
D55V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                1                 44
  CLUS_3                1                 11
  CLUS_4                2                 31

Clustering(56) Variable = 19q loss mutation analysis
D56V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0    0
  19Q LOSS WILD-TYPE    7    9
D56V2, multiclass
D56V3, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                 22
  CLUS_2                0                 20
  CLUS_3                1                 27
  CLUS_4                0                 45
D56V4, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 20
  CLUS_2                0                 27
  CLUS_3                2                 37
D56V5, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                 75 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-B3-3925 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5876         TCGA-BQ-5877 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7056         TCGA-BQ-7058 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-GL-6846         TCGA-GL-7966 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HE-7128         TCGA-HE-7129         TCGA-HE-7130 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D56V6, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                 75 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-B3-3925 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5876         TCGA-BQ-5877 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7056         TCGA-BQ-7058 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-GL-6846         TCGA-GL-7966 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HE-7128         TCGA-HE-7129         TCGA-HE-7130 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D56V7, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                0                 38
  CLUS_3                1                 34
  CLUS_4                0                 17
D56V8, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                1                 44
  CLUS_3                0                 12
  CLUS_4                2                 31

Clustering(57) Variable = 21q loss mutation analysis
D57V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2    1
  21Q LOSS WILD-TYPE    5    8
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                  5
  CLUS_2                1                  8
D57V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                0                  4
  CLUS_2                1                  6
  CLUS_3                2                  3
D57V3, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 22
  CLUS_2                2                 18
  CLUS_3                5                 23
  CLUS_4                3                 42
D57V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 19
  CLUS_2                4                 23
  CLUS_3                2                 37
D57V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 24
  CLUS_2                1                 23
  CLUS_3                5                 20
D57V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                5                 32
  CLUS_3                3                 18
D57V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                3                 35
  CLUS_3                4                 31
  CLUS_4                4                 13
D57V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                5                 22
  CLUS_2                3                 42
  CLUS_3                0                 12
  CLUS_4                4                 29

Clustering(58) Variable = 22q loss mutation analysis
D58V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1    1
  22Q LOSS WILD-TYPE    6    8
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                  6
  CLUS_2                1                  8
D58V2, multiclass
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 2                 14 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B3-3925 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
D58V3, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                 22
  CLUS_2                1                 19
  CLUS_3               11                 17
  CLUS_4                7                 38
D58V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                 19
  CLUS_2                9                 18
  CLUS_3                6                 33
D58V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                4                 23
  CLUS_2                6                 18
  CLUS_3                5                 20
D58V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                4                 33
  CLUS_3                8                 13
D58V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                5                 22
  CLUS_2                4                 34
  CLUS_3                6                 29
  CLUS_4                6                 11
D58V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                6                 21
  CLUS_2                5                 40
  CLUS_3                2                 10
  CLUS_4                8                 25

Clustering(59) Variable = Xq loss mutation analysis
D59V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    1
  XQ LOSS WILD-TYPE    7    8
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                 7
  CLUS_2               1                 8
D59V2, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D59V3, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                23
  CLUS_2               1                19
  CLUS_3               1                27
  CLUS_4               0                45
D59V4, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                85 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7584        TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-7915        TCGA-A4-7996        TCGA-A4-7997 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B9-5156 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7773 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GL-7966        TCGA-HE-7128        TCGA-HE-7129        TCGA-HE-7130 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-J7-6720 
"XQ LOSS WILD-TYPE" 
D59V5, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                74 
       TCGA-A4-7997        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B3-3925        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5156        TCGA-BQ-5876        TCGA-BQ-5877 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966        TCGA-HE-7128 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HE-7129        TCGA-HE-7130 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D59V6, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                74 
       TCGA-A4-7997        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B3-3925        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5156        TCGA-BQ-5876        TCGA-BQ-5877 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966        TCGA-HE-7128 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HE-7129        TCGA-HE-7130 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D59V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               1                37
  CLUS_3               2                33
  CLUS_4               0                17
D59V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               0                45
  CLUS_3               1                11
  CLUS_4               2                31
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"               "CN_CNMF" 
                     V4                      V5                      V6 
     "METHLYATION_CNMF"          "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL" 
                     V7                      V8 
          "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
