
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/399246/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SKCM-Regional_LN/3157616/1.GDAC_mergedClustering.Finished/SKCM-Regional_LN.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-Regional_LN", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"                  "-oT=SKCM-Regional_LN"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=116, in cluster file=112, common to both=112
[1] "Reduce the number of clustering variables from 80 to 72."
[1]  72 112
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               12               100 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               12               100 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               33                79 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               33                79 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10               102 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10               102 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                9               103 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                9               103 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                7               105 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                7               105 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               104 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8               104 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10               102 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10               102 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10               102 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10               102 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               12               100 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               12               100 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5               107 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5               107 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               35                77 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               35                77 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8               104 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8               104 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               44                68 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               44                68 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               44                68 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               44                68 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               18                94 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               18                94 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               31                81 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               31                81 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               108 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4               108 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                104 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                104 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                107 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                107 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                10                102 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                10                102 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                108 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                108 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                 97 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                 97 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 9                103 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 9                103 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                16                 96 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                16                 96 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                106 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                106 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                106 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                106 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                104 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                104 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                15                 97 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                15                 97 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                14                 98 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                14                 98 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                106 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                106 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 8                104 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 8                104 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                103 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                103 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                31                 81 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                31                 81 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                39                 73 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                39                 73 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                11                101 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                11                101 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                24                 88 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                24                 88 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                8               104 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                8               104 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               12               100 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               12               100 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               11               101 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               11               101 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5               107 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5               107 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                8               104 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                8               104 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9               103 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9               103 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10               102 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10               102 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               14                98 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               14                98 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               24                88 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               24                88 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                9               103 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                9               103 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               40                72 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               40                72 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               14                98 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               14                98 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               109 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               109 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               57                55 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               57                55 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               42                70 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               42                70 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                45                 67 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                45                 67 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                49                 63 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                49                 63 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                26                 86 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                26                 86 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                30                 82 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                30                 82 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                107 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                107 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                104 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                104 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                17                 95 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                17                 95 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                25                 87 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                25                 87 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                105 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                105 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 8                104 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 8                104 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                16                 96 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                16                 96 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                28                 84 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                28                 84 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                13                 99 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                13                 99 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                18                 94 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                18                 94 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                18                 94 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                18                 94 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                12                100 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                12                100 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                100 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                100 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                109 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                109 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 97 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 97 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 7                105 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 7                105 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               109 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               109 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "RPPA_CNMF"            
[4] "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 8 rows and 112 columns.

Variable 1:'CN_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'RPPA_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "RPPA_CNMF"            
[4] "RPPA_CHIERARCHICAL"    "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 112 columns, 0 survival variables, and 8 non-survival variables.
CN_CNMF, nv=4, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=5, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               6                24
  CLUS_2               1                17
  CLUS_3               4                34
  CLUS_4               1                25
D1V2, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               0                40
  CLUS_3               3                23
  CLUS_4               8                20
D1V3, multiclass
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                12
  CLUS_2               3                19
  CLUS_3               5                29
  CLUS_4               1                11
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3                39
  CLUS_2               1                26
  CLUS_3               8                35
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               1                28
  CLUS_3               2                32
  CLUS_4               5                26
D1V7, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               7                35
  CLUS_2               3                20
  CLUS_3               2                43
D1V8, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                10
  CLUS_2               0                25
  CLUS_3              11                63

Clustering(2) Variable = 1q gain mutation analysis
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              15                15
  CLUS_2               2                16
  CLUS_3               8                30
  CLUS_4               8                18
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               6                12
  CLUS_2               7                33
  CLUS_3               9                17
  CLUS_4              11                17
D2V3, multiclass
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               7                15
  CLUS_3               9                25
  CLUS_4               5                 7
D2V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              11                31
  CLUS_2               3                24
  CLUS_3              19                24
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               8                10
  CLUS_2               4                25
  CLUS_3               8                26
  CLUS_4              13                18
D2V7, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              15                27
  CLUS_2               8                15
  CLUS_3               9                36
D2V8, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3                 8
  CLUS_2               4                21
  CLUS_3              25                49

Clustering(3) Variable = 2p gain mutation analysis
D3V1, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               5                25
  CLUS_2               1                17
  CLUS_3               2                36
  CLUS_4               2                24
D3V2, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               3                37
  CLUS_3               2                24
  CLUS_4               3                25
D3V3, multiclass
D3V4, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               0                12
  CLUS_2               2                20
  CLUS_3               3                31
  CLUS_4               2                10
D3V5, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               3                39
  CLUS_2               1                26
  CLUS_3               6                37
D3V6, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               2                27
  CLUS_3               3                31
  CLUS_4               2                29
D3V7, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               4                38
  CLUS_2               1                22
  CLUS_3               4                41
D3V8, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                10
  CLUS_2               3                22
  CLUS_3               5                69

Clustering(4) Variable = 2q gain mutation analysis
D4V1, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               4                26
  CLUS_2               1                17
  CLUS_3               2                36
  CLUS_4               2                24
D4V2, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               3                37
  CLUS_3               2                24
  CLUS_4               2                26
D4V3, multiclass
D4V4, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                12
  CLUS_2               2                20
  CLUS_3               3                31
  CLUS_4               2                10
D4V5, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               3                39
  CLUS_2               1                26
  CLUS_3               5                38
D4V6, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               2                27
  CLUS_3               3                31
  CLUS_4               1                30
D4V7, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               3                39
  CLUS_2               1                22
  CLUS_3               4                41
D4V8, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                10
  CLUS_2               3                22
  CLUS_3               4                70

Clustering(5) Variable = 3p gain mutation analysis
D5V1, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                28
  CLUS_2               4                14
  CLUS_3               0                38
  CLUS_4               1                25
D5V2, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               0                40
  CLUS_3               4                22
  CLUS_4               1                27
D5V3, multiclass
D5V4, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               1                11
  CLUS_2               0                22
  CLUS_3               3                31
  CLUS_4               1                11
D5V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4                38
  CLUS_2               0                27
  CLUS_3               3                40
D5V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               0                29
  CLUS_3               3                31
  CLUS_4               2                29
D5V7, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               3                39
  CLUS_2               1                22
  CLUS_3               3                42
D5V8, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                11
  CLUS_2               2                23
  CLUS_3               5                69

Clustering(6) Variable = 3q gain mutation analysis
D6V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2                28
  CLUS_2               4                14
  CLUS_3               0                38
  CLUS_4               2                24
D6V2, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               1                39
  CLUS_3               4                22
  CLUS_4               1                27
D6V3, multiclass
D6V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2                10
  CLUS_2               0                22
  CLUS_3               2                32
  CLUS_4               1                11
D6V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               6                36
  CLUS_2               0                27
  CLUS_3               2                41
D6V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               1                28
  CLUS_3               3                31
  CLUS_4               0                31
D6V7, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                39
  CLUS_2               2                21
  CLUS_3               3                42
D6V8, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               1                10
  CLUS_2               2                23
  CLUS_3               5                69

Clustering(7) Variable = 4p gain mutation analysis
D7V1, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               5                25
  CLUS_2               2                16
  CLUS_3               1                37
  CLUS_4               2                24
D7V2, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               0                40
  CLUS_3               5                21
  CLUS_4               2                26
D7V3, multiclass
D7V4, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                10
  CLUS_2               1                21
  CLUS_3               4                30
  CLUS_4               0                12
D7V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4                38
  CLUS_2               1                26
  CLUS_3               5                38
D7V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               2                27
  CLUS_3               2                32
  CLUS_4               3                28
D7V7, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               4                38
  CLUS_2               5                18
  CLUS_3               1                44
D7V8, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               2                23
  CLUS_3               6                68

Clustering(8) Variable = 4q gain mutation analysis
D8V1, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               7                23
  CLUS_2               2                16
  CLUS_3               0                38
  CLUS_4               1                25
D8V2, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               0                40
  CLUS_3               4                22
  CLUS_4               4                24
D8V3, multiclass
D8V4, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2                10
  CLUS_2               1                21
  CLUS_3               3                31
  CLUS_4               0                12
D8V5, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               3                39
  CLUS_2               1                26
  CLUS_3               6                37
D8V6, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               2                27
  CLUS_3               2                32
  CLUS_4               4                27
D8V7, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               4                38
  CLUS_2               5                18
  CLUS_3               1                44
D8V8, multiclass
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               2                23
  CLUS_3               6                68

Clustering(9) Variable = 5p gain mutation analysis
D9V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                29
  CLUS_2               5                13
  CLUS_3               2                36
  CLUS_4               4                22
D9V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               3                37
  CLUS_3               4                22
  CLUS_4               2                26
D9V3, multiclass
D9V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               1                11
  CLUS_2               2                20
  CLUS_3               5                29
  CLUS_4               2                10
D9V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               7                35
  CLUS_2               1                26
  CLUS_3               4                39
D9V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               1                28
  CLUS_3               6                28
  CLUS_4               2                29
D9V7, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               4                38
  CLUS_2               5                18
  CLUS_3               3                42
D9V8, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               3                22
  CLUS_3               7                67

Clustering(10) Variable = 5q gain mutation analysis
D10V1, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                29
  CLUS_2               2                16
  CLUS_3               0                38
  CLUS_4               2                24
D10V2, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               0                40
  CLUS_3               2                24
  CLUS_4               1                27
D10V3, multiclass
D10V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                12
  CLUS_2               1                21
  CLUS_3               4                30
  CLUS_4               0                12
D10V5, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                39
  CLUS_2               0                27
  CLUS_3               2                41
D10V6, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               0                29
  CLUS_3               3                31
  CLUS_4               1                30
D10V7, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                39
  CLUS_2               1                22
  CLUS_3               1                44
D10V8, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                11
  CLUS_2               1                24
  CLUS_3               4                70

Clustering(11) Variable = 6p gain mutation analysis
D11V1, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              18                12
  CLUS_2               4                14
  CLUS_3               7                31
  CLUS_4               6                20
D11V2, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               7                33
  CLUS_3              13                13
  CLUS_4              11                17
D11V3, multiclass
D11V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               5                 7
  CLUS_2               8                14
  CLUS_3              11                23
  CLUS_4               3                 9
D11V5, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              16                26
  CLUS_2               7                20
  CLUS_3              12                31
D11V6, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               7                22
  CLUS_3              11                23
  CLUS_4              13                18
D11V7, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1              16                26
  CLUS_2               6                17
  CLUS_3              13                32
D11V8, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               4                 7
  CLUS_2               3                22
  CLUS_3              28                46

Clustering(12) Variable = 6q gain mutation analysis
D12V1, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               4                26
  CLUS_2               1                17
  CLUS_3               2                36
  CLUS_4               1                25
D12V2, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               2                16
  CLUS_2               3                37
  CLUS_3               2                24
  CLUS_4               1                27
D12V3, multiclass
D12V4, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                11
  CLUS_2               2                20
  CLUS_3               2                32
  CLUS_4               1                11
D12V5, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               5                37
  CLUS_2               2                25
  CLUS_3               1                42
D12V6, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               1                28
  CLUS_3               4                30
  CLUS_4               2                29
D12V7, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               3                39
  CLUS_2               0                23
  CLUS_3               5                40
D12V8, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                11
  CLUS_2               1                24
  CLUS_3               7                67

Clustering(13) Variable = 7p gain mutation analysis
D13V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              14                16
  CLUS_2              14                 4
  CLUS_3               7                31
  CLUS_4               9                17
D13V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              10                 8
  CLUS_2              10                30
  CLUS_3              15                11
  CLUS_4               9                19
D13V3, multiclass
D13V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               6                 6
  CLUS_2               8                14
  CLUS_3              12                22
  CLUS_4               7                 5
D13V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              21                21
  CLUS_2               5                22
  CLUS_3              18                25
D13V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               7                11
  CLUS_2               8                21
  CLUS_3              17                17
  CLUS_4              12                19
D13V7, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              18                24
  CLUS_2              12                11
  CLUS_3              14                31
D13V8, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               7                 4
  CLUS_2               7                18
  CLUS_3              30                44

Clustering(14) Variable = 7q gain mutation analysis
D14V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              10                20
  CLUS_2              15                 3
  CLUS_3               9                29
  CLUS_4              10                16
D14V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              12                 6
  CLUS_2              12                28
  CLUS_3              15                11
  CLUS_4               5                23
D14V3, multiclass
D14V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               6                 6
  CLUS_2               7                15
  CLUS_3              11                23
  CLUS_4               7                 5
D14V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              23                19
  CLUS_2               7                20
  CLUS_3              14                29
D14V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               7                11
  CLUS_2              10                19
  CLUS_3              19                15
  CLUS_4               8                23
D14V7, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              15                27
  CLUS_2              14                 9
  CLUS_3              15                30
D14V8, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               8                 3
  CLUS_2               9                16
  CLUS_3              27                47

Clustering(15) Variable = 8p gain mutation analysis
D15V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               3                27
  CLUS_2              10                 8
  CLUS_3               1                37
  CLUS_4               4                22
D15V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               6                12
  CLUS_2               2                38
  CLUS_3               8                18
  CLUS_4               2                26
D15V3, multiclass
D15V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                12
  CLUS_2               5                17
  CLUS_3               7                27
  CLUS_4               3                 9
D15V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              13                29
  CLUS_2               2                25
  CLUS_3               3                40
D15V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               3                26
  CLUS_3              10                24
  CLUS_4               4                27
D15V7, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               5                37
  CLUS_2               4                19
  CLUS_3               9                36
D15V8, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               0                11
  CLUS_2               6                19
  CLUS_3              12                62

Clustering(16) Variable = 8q gain mutation analysis
D16V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              10                20
  CLUS_2              12                 6
  CLUS_3               2                36
  CLUS_4               7                19
D16V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              11                 7
  CLUS_2               3                37
  CLUS_3              12                14
  CLUS_4               5                23
D16V3, multiclass
D16V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               2                10
  CLUS_2               7                15
  CLUS_3              11                23
  CLUS_4               5                 7
D16V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              20                22
  CLUS_2               2                25
  CLUS_3               9                34
D16V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               4                14
  CLUS_2               3                26
  CLUS_3              15                19
  CLUS_4               9                22
D16V7, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              11                31
  CLUS_2               6                17
  CLUS_3              14                31
D16V8, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               1                10
  CLUS_2               9                16
  CLUS_3              21                53

Clustering(17) Variable = 9q gain mutation analysis
D17V1, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                29
  CLUS_2               0                18
  CLUS_3               1                37
  CLUS_4               2                24
D17V2, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                17
  CLUS_2               1                39
  CLUS_3               1                25
  CLUS_4               1                27
D17V3, multiclass
D17V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                12
  CLUS_2               0                22
  CLUS_3               3                31
  CLUS_4               0                12
D17V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                42
  CLUS_2               0                27
  CLUS_3               4                39
D17V6, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3                15
  CLUS_2               0                29
  CLUS_3               0                34
  CLUS_4               1                30
D17V7, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                41
  CLUS_2               2                21
  CLUS_3               0                45
D17V8, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                10
  CLUS_2               0                25
  CLUS_3               2                72

Clustering(18) Variable = 11p gain mutation analysis
D18V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                 27
  CLUS_2                2                 16
  CLUS_3                1                 37
  CLUS_4                2                 24
D18V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                2                 38
  CLUS_3                3                 23
  CLUS_4                0                 28
D18V3, multiclass
D18V4, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                2                 20
  CLUS_3                1                 33
  CLUS_4                1                 11
D18V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                6                 36
  CLUS_2                1                 26
  CLUS_3                1                 42
D18V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 28
  CLUS_3                5                 29
  CLUS_4                0                 31
D18V7, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 41
  CLUS_2                2                 21
  CLUS_3                5                 40
D18V8, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                6                 19
  CLUS_3                1                 73

Clustering(19) Variable = 11q gain mutation analysis
D19V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                 28
  CLUS_2                1                 17
  CLUS_3                0                 38
  CLUS_4                2                 24
D19V2, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 39
  CLUS_3                2                 24
  CLUS_4                0                 28
D19V3, multiclass
D19V4, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 12
  CLUS_2                2                 20
  CLUS_3                1                 33
  CLUS_4                0                 12
D19V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                 38
  CLUS_2                1                 26
  CLUS_3                0                 43
D19V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                 28
  CLUS_3                3                 31
  CLUS_4                0                 31
D19V7, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 41
  CLUS_2                1                 22
  CLUS_3                3                 42
D19V8, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                4                 21
  CLUS_3                1                 73

Clustering(20) Variable = 12p gain mutation analysis
D20V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                 28
  CLUS_2                4                 14
  CLUS_3                0                 38
  CLUS_4                4                 22
D20V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                2                 38
  CLUS_3                5                 21
  CLUS_4                0                 28
D20V3, multiclass
D20V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                2                 20
  CLUS_3                3                 31
  CLUS_4                1                 11
D20V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                7                 35
  CLUS_2                0                 27
  CLUS_3                3                 40
D20V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                 28
  CLUS_3                5                 29
  CLUS_4                1                 30
D20V7, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                 40
  CLUS_2                5                 18
  CLUS_3                3                 42
D20V8, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                3                 22
  CLUS_3                5                 69

Clustering(21) Variable = 12q gain mutation analysis
D21V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 29
  CLUS_2                2                 16
  CLUS_3                0                 38
  CLUS_4                1                 25
D21V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                0                 40
  CLUS_3                2                 24
  CLUS_4                0                 28
D21V3, multiclass
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 78 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A2J6         TCGA-D3-A2J8 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A3CE         TCGA-D9-A148 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D9-A1JW         TCGA-D9-A1JX         TCGA-DA-A1HV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I2 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1IB         TCGA-EE-A17X         TCGA-EE-A181 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29E         TCGA-EE-A29H         TCGA-EE-A29L 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29R 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A2A0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-EE-A2GC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GI         TCGA-EE-A2GK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2GL         TCGA-EE-A2GS         TCGA-EE-A2GT 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2GU         TCGA-EE-A2M5         TCGA-EE-A2M6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2MC         TCGA-EE-A2MD 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2MI         TCGA-EE-A2MJ         TCGA-EE-A2MK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2ML         TCGA-EE-A2MM         TCGA-EE-A2MN 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2MP         TCGA-EE-A2MR         TCGA-EE-A2MS 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2MT         TCGA-EE-A3AA         TCGA-EE-A3AB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A3AC         TCGA-EE-A3AD         TCGA-EE-A3AE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A3AF         TCGA-ER-A19F         TCGA-ER-A19J 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A19O         TCGA-ER-A1A1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1YW         TCGA-FS-A1Z4         TCGA-FS-A1ZD 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZG         TCGA-FS-A1ZH         TCGA-FS-A1ZJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-GN-A264         TCGA-GN-A265 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26D 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
D21V4, multiclass
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 78 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A2J6         TCGA-D3-A2J8 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A3CE         TCGA-D9-A148 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D9-A1JW         TCGA-D9-A1JX         TCGA-DA-A1HV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I2 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1IB         TCGA-EE-A17X         TCGA-EE-A181 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29E         TCGA-EE-A29H         TCGA-EE-A29L 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29N         TCGA-EE-A29P         TCGA-EE-A29R 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A2A0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A6         TCGA-EE-A2GC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2GH         TCGA-EE-A2GI         TCGA-EE-A2GK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2GL         TCGA-EE-A2GS         TCGA-EE-A2GT 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2GU         TCGA-EE-A2M5         TCGA-EE-A2M6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2M8         TCGA-EE-A2MC         TCGA-EE-A2MD 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2MI         TCGA-EE-A2MJ         TCGA-EE-A2MK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2ML         TCGA-EE-A2MM         TCGA-EE-A2MN 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2MP         TCGA-EE-A2MR         TCGA-EE-A2MS 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2MT         TCGA-EE-A3AA         TCGA-EE-A3AB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A3AC         TCGA-EE-A3AD         TCGA-EE-A3AE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A3AF         TCGA-ER-A19F         TCGA-ER-A19J 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A19O         TCGA-ER-A1A1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1YW         TCGA-FS-A1Z4         TCGA-FS-A1ZD 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZG         TCGA-FS-A1ZH         TCGA-FS-A1ZJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-GN-A264         TCGA-GN-A265 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26D 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
D21V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 40
  CLUS_2                0                 27
  CLUS_3                2                 41
D21V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                0                 29
  CLUS_3                2                 32
  CLUS_4                0                 31
D21V7, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                 42
  CLUS_2                3                 20
  CLUS_3                1                 44
D21V8, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                1                 24
  CLUS_3                1                 73

Clustering(22) Variable = 13q gain mutation analysis
D22V1, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                6                 24
  CLUS_2                4                 14
  CLUS_3                0                 38
  CLUS_4                5                 21
D22V2, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                5                 13
  CLUS_2                2                 38
  CLUS_3                5                 21
  CLUS_4                3                 25
D22V3, multiclass
D22V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                2                 20
  CLUS_3                5                 29
  CLUS_4                3                  9
D22V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                9                 33
  CLUS_2                1                 26
  CLUS_3                5                 38
D22V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                3                 26
  CLUS_3                5                 29
  CLUS_4                4                 27
D22V7, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                5                 37
  CLUS_2                3                 20
  CLUS_3                7                 38
D22V8, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                2                 23
  CLUS_3               11                 63

Clustering(23) Variable = 14q gain mutation analysis
D23V1, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                 28
  CLUS_2                4                 14
  CLUS_3                2                 36
  CLUS_4                1                 25
D23V2, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                2                 38
  CLUS_3                4                 22
  CLUS_4                1                 27
D23V3, multiclass
D23V4, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                1                 21
  CLUS_3                6                 28
  CLUS_4                0                 12
D23V5, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                5                 37
  CLUS_2                0                 27
  CLUS_3                4                 39
D23V6, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                0                 29
  CLUS_3                3                 31
  CLUS_4                2                 29
D23V7, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                4                 38
  CLUS_2                2                 21
  CLUS_3                3                 42
D23V8, multiclass
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                0                 25
  CLUS_3                8                 66

Clustering(24) Variable = 15q gain mutation analysis
D24V1, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                2                 28
  CLUS_2                8                 10
  CLUS_3                3                 35
  CLUS_4                3                 23
D24V2, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                6                 34
  CLUS_3                5                 21
  CLUS_4                2                 26
D24V3, multiclass
D24V4, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                 12
  CLUS_2                4                 18
  CLUS_3                5                 29
  CLUS_4                0                 12
D24V5, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                6                 36
  CLUS_2                3                 24
  CLUS_3                7                 36
D24V6, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                5                 13
  CLUS_2                3                 26
  CLUS_3                5                 29
  CLUS_4                3                 28
D24V7, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                5                 37
  CLUS_2                5                 18
  CLUS_3                5                 40
D24V8, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                6                 19
  CLUS_3                8                 66

Clustering(25) Variable = 16p gain mutation analysis
D25V1, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 29
  CLUS_2                3                 15
  CLUS_3                0                 38
  CLUS_4                2                 24
D25V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                1                 39
  CLUS_3                5                 21
  CLUS_4                0                 28
D25V3, multiclass
D25V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                 12
  CLUS_2                1                 21
  CLUS_3                2                 32
  CLUS_4                1                 11
D25V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                4                 38
  CLUS_2                0                 27
  CLUS_3                2                 41
D25V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                0                 29
  CLUS_3                3                 31
  CLUS_4                0                 31
D25V7, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 41
  CLUS_2                3                 20
  CLUS_3                2                 43
D25V8, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                2                 23
  CLUS_3                3                 71

Clustering(26) Variable = 16q gain mutation analysis
D26V1, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 29
  CLUS_2                2                 16
  CLUS_3                0                 38
  CLUS_4                3                 23
D26V2, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                2                 38
  CLUS_3                4                 22
  CLUS_4                0                 28
D26V3, multiclass
D26V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                 12
  CLUS_2                1                 21
  CLUS_3                1                 33
  CLUS_4                2                 10
D26V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                4                 38
  CLUS_2                1                 26
  CLUS_3                1                 42
D26V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 28
  CLUS_3                3                 31
  CLUS_4                0                 31
D26V7, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                 42
  CLUS_2                4                 19
  CLUS_3                2                 43
D26V8, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                2                 23
  CLUS_3                2                 72

Clustering(27) Variable = 17p gain mutation analysis
D27V1, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                 27
  CLUS_2                1                 17
  CLUS_3                1                 37
  CLUS_4                3                 23
D27V2, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                2                 38
  CLUS_3                2                 24
  CLUS_4                1                 27
D27V3, multiclass
D27V4, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                4                  8
  CLUS_2                2                 20
  CLUS_3                1                 33
  CLUS_4                1                 11
D27V5, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                5                 37
  CLUS_2                1                 26
  CLUS_3                2                 41
D27V6, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                3                 26
  CLUS_3                3                 31
  CLUS_4                1                 30
D27V7, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                3                 39
  CLUS_2                3                 20
  CLUS_3                2                 43
D27V8, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                2                 23
  CLUS_3                5                 69

Clustering(28) Variable = 17q gain mutation analysis
D28V1, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                7                 23
  CLUS_2                2                 16
  CLUS_3                1                 37
  CLUS_4                5                 21
D28V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                2                 38
  CLUS_3                3                 23
  CLUS_4                6                 22
D28V3, multiclass
D28V4, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                4                  8
  CLUS_2                3                 19
  CLUS_3                6                 28
  CLUS_4                1                 11
D28V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                5                 37
  CLUS_2                2                 25
  CLUS_3                8                 35
D28V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                4                 25
  CLUS_3                3                 31
  CLUS_4                5                 26
D28V7, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                9                 33
  CLUS_2                4                 19
  CLUS_3                2                 43
D28V8, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                2                 23
  CLUS_3               12                 62

Clustering(29) Variable = 18p gain mutation analysis
D29V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                5                 25
  CLUS_2                4                 14
  CLUS_3                1                 37
  CLUS_4                4                 22
D29V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                5                 13
  CLUS_2                1                 39
  CLUS_3                5                 21
  CLUS_4                3                 25
D29V3, multiclass
D29V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                 10
  CLUS_2                2                 20
  CLUS_3                7                 27
  CLUS_4                2                 10
D29V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                5                 37
  CLUS_2                1                 26
  CLUS_3                8                 35
D29V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                2                 27
  CLUS_3                3                 31
  CLUS_4                6                 25
D29V7, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                5                 37
  CLUS_2                7                 16
  CLUS_3                2                 43
D29V8, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                3                  8
  CLUS_2                2                 23
  CLUS_3                9                 65

Clustering(30) Variable = 18q gain mutation analysis
D30V1, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 27
  CLUS_2                2                 16
  CLUS_3                1                 37
  CLUS_4                0                 26
D30V2, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                1                 39
  CLUS_3                0                 26
  CLUS_4                2                 26
D30V3, multiclass
D30V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                2                 20
  CLUS_3                2                 32
  CLUS_4                1                 11
D30V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                 40
  CLUS_2                0                 27
  CLUS_3                4                 39
D30V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                0                 29
  CLUS_3                1                 33
  CLUS_4                4                 27
D30V7, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                2                 40
  CLUS_2                2                 21
  CLUS_3                2                 43
D30V8, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                1                 24
  CLUS_3                5                 69

Clustering(31) Variable = 19p gain mutation analysis
D31V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 28
  CLUS_2                3                 15
  CLUS_3                1                 37
  CLUS_4                2                 24
D31V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                0                 40
  CLUS_3                4                 22
  CLUS_4                2                 26
D31V3, multiclass
D31V4, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 12
  CLUS_2                4                 18
  CLUS_3                3                 31
  CLUS_4                1                 11
D31V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                7                 35
  CLUS_2                0                 27
  CLUS_3                1                 42
D31V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                0                 29
  CLUS_3                7                 27
  CLUS_4                1                 30
D31V7, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 40
  CLUS_2                3                 20
  CLUS_3                3                 42
D31V8, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                4                 21
  CLUS_3                4                 70

Clustering(32) Variable = 19q gain mutation analysis
D32V1, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                3                 27
  CLUS_2                4                 14
  CLUS_3                0                 38
  CLUS_4                2                 24
D32V2, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                0                 40
  CLUS_3                4                 22
  CLUS_4                1                 27
D32V3, multiclass
D32V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                3                 19
  CLUS_3                3                 31
  CLUS_4                2                 10
D32V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                8                 34
  CLUS_2                0                 27
  CLUS_3                1                 42
D32V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                0                 29
  CLUS_3                8                 26
  CLUS_4                1                 30
D32V7, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 40
  CLUS_2                3                 20
  CLUS_3                4                 41
D32V8, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                5                 20
  CLUS_3                4                 70

Clustering(33) Variable = 20p gain mutation analysis
D33V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                6                 24
  CLUS_2               10                  8
  CLUS_3                2                 36
  CLUS_4               13                 13
D33V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               10                  8
  CLUS_2                6                 34
  CLUS_3               12                 14
  CLUS_4                3                 25
D33V3, multiclass
D33V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                3                  9
  CLUS_2                6                 16
  CLUS_3               11                 23
  CLUS_4                3                  9
D33V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               18                 24
  CLUS_2                2                 25
  CLUS_3               11                 32
D33V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                7                 11
  CLUS_2                3                 26
  CLUS_3               14                 20
  CLUS_4                7                 24
D33V7, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               10                 32
  CLUS_2               10                 13
  CLUS_3               11                 34
D33V8, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                4                  7
  CLUS_2                7                 18
  CLUS_3               20                 54

Clustering(34) Variable = 20q gain mutation analysis
D34V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               11                 19
  CLUS_2               11                  7
  CLUS_3                3                 35
  CLUS_4               14                 12
D34V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               12                  6
  CLUS_2                7                 33
  CLUS_3               13                 13
  CLUS_4                7                 21
D34V3, multiclass
D34V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                5                  7
  CLUS_2                6                 16
  CLUS_3               15                 19
  CLUS_4                4                  8
D34V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               20                 22
  CLUS_2                3                 24
  CLUS_3               16                 27
D34V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                9                  9
  CLUS_2                5                 24
  CLUS_3               15                 19
  CLUS_4               10                 21
D34V7, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               16                 26
  CLUS_2               11                 12
  CLUS_3               11                 34
D34V8, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                5                  6
  CLUS_2                7                 18
  CLUS_3               26                 48

Clustering(35) Variable = 21q gain mutation analysis
D35V1, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                 27
  CLUS_2                2                 16
  CLUS_3                2                 36
  CLUS_4                4                 22
D35V2, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                5                 13
  CLUS_2                2                 38
  CLUS_3                1                 25
  CLUS_4                3                 25
D35V3, multiclass
D35V4, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                0                 12
  CLUS_2                2                 20
  CLUS_3                3                 31
  CLUS_4                2                 10
D35V5, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                5                 37
  CLUS_2                1                 26
  CLUS_3                5                 38
D35V6, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                 28
  CLUS_3                5                 29
  CLUS_4                4                 27
D35V7, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                3                 39
  CLUS_2                2                 21
  CLUS_3                6                 39
D35V8, multiclass
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                2                 23
  CLUS_3                8                 66

Clustering(36) Variable = 22q gain mutation analysis
D36V1, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                7                 23
  CLUS_2                7                 11
  CLUS_3                7                 31
  CLUS_4                3                 23
D36V2, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                6                 12
  CLUS_2                7                 33
  CLUS_3                7                 19
  CLUS_4                4                 24
D36V3, multiclass
D36V4, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                4                  8
  CLUS_2                3                 19
  CLUS_3                7                 27
  CLUS_4                4                  8
D36V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                8                 34
  CLUS_2                5                 22
  CLUS_3               11                 32
D36V6, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                8                 10
  CLUS_2                4                 25
  CLUS_3                7                 27
  CLUS_4                5                 26
D36V7, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                8                 34
  CLUS_2                6                 17
  CLUS_3                9                 36
D36V8, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                4                 21
  CLUS_3               17                 57

Clustering(37) Variable = 1p loss mutation analysis
D37V1, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3                27
  CLUS_2               1                17
  CLUS_3               0                38
  CLUS_4               4                22
D37V2, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               1                39
  CLUS_3               3                23
  CLUS_4               1                27
D37V3, multiclass
D37V4, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0                12
  CLUS_2               1                21
  CLUS_3               5                29
  CLUS_4               1                11
D37V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               4                38
  CLUS_2               0                27
  CLUS_3               4                39
D37V6, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               0                29
  CLUS_3               4                30
  CLUS_4               2                29
D37V7, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               3                39
  CLUS_2               2                21
  CLUS_3               3                42
D37V8, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               1                10
  CLUS_2               0                25
  CLUS_3               7                67

Clustering(38) Variable = 2p loss mutation analysis
D38V1, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               5                25
  CLUS_2               2                16
  CLUS_3               1                37
  CLUS_4               4                22
D38V2, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               2                38
  CLUS_3               6                20
  CLUS_4               2                26
D38V3, multiclass
D38V4, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                11
  CLUS_2               1                21
  CLUS_3               7                27
  CLUS_4               0                12
D38V5, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               7                35
  CLUS_2               1                26
  CLUS_3               4                39
D38V6, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               2                27
  CLUS_3               4                30
  CLUS_4               3                28
D38V7, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               9                33
  CLUS_2               1                22
  CLUS_3               2                43
D38V8, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                11
  CLUS_2               0                25
  CLUS_3              12                62

Clustering(39) Variable = 2q loss mutation analysis
D39V1, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               4                26
  CLUS_2               0                18
  CLUS_3               1                37
  CLUS_4               6                20
D39V2, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               1                39
  CLUS_3               4                22
  CLUS_4               4                24
D39V3, multiclass
D39V4, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                11
  CLUS_2               2                20
  CLUS_3               5                29
  CLUS_4               0                12
D39V5, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               6                36
  CLUS_2               1                26
  CLUS_3               4                39
D39V6, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               2                27
  CLUS_3               3                31
  CLUS_4               3                28
D39V7, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               8                34
  CLUS_2               1                22
  CLUS_3               2                43
D39V8, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                11
  CLUS_2               0                25
  CLUS_3              11                63

Clustering(40) Variable = 3p loss mutation analysis
D40V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                29
  CLUS_2               4                14
  CLUS_3               0                38
  CLUS_4               0                26
D40V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               1                39
  CLUS_3               3                23
  CLUS_4               0                28
D40V3, multiclass
D40V4, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                12
  CLUS_2               2                20
  CLUS_3               2                32
  CLUS_4               0                12
D40V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               4                38
  CLUS_2               0                27
  CLUS_3               1                42
D40V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               0                29
  CLUS_3               4                30
  CLUS_4               0                31
D40V7, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               2                40
  CLUS_2               2                21
  CLUS_3               1                44
D40V8, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                11
  CLUS_2               2                23
  CLUS_3               3                71

Clustering(41) Variable = 3q loss mutation analysis
D41V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               3                27
  CLUS_2               4                14
  CLUS_3               0                38
  CLUS_4               1                25
D41V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               1                39
  CLUS_3               3                23
  CLUS_4               3                25
D41V3, multiclass
D41V4, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                12
  CLUS_2               1                21
  CLUS_3               5                29
  CLUS_4               0                12
D41V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               3                39
  CLUS_2               0                27
  CLUS_3               5                38
D41V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               0                29
  CLUS_3               3                31
  CLUS_4               4                27
D41V7, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               5                37
  CLUS_2               1                22
  CLUS_3               2                43
D41V8, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                11
  CLUS_2               1                24
  CLUS_3               7                67

Clustering(42) Variable = 4p loss mutation analysis
D42V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               4                26
  CLUS_2               2                16
  CLUS_3               2                36
  CLUS_4               1                25
D42V2, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               4                14
  CLUS_2               2                38
  CLUS_3               0                26
  CLUS_4               3                25
D42V3, multiclass
D42V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                12
  CLUS_2               1                21
  CLUS_3               4                30
  CLUS_4               2                10
D42V5, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               3                39
  CLUS_2               0                27
  CLUS_3               6                37
D42V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               0                29
  CLUS_3               3                31
  CLUS_4               3                28
D42V7, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               6                36
  CLUS_2               0                23
  CLUS_3               3                42
D42V8, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                11
  CLUS_2               0                25
  CLUS_3               9                65

Clustering(43) Variable = 4q loss mutation analysis
D43V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               3                27
  CLUS_2               3                15
  CLUS_3               3                35
  CLUS_4               1                25
D43V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               3                37
  CLUS_3               1                25
  CLUS_4               3                25
D43V3, multiclass
D43V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                12
  CLUS_2               2                20
  CLUS_3               4                30
  CLUS_4               2                10
D43V5, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               4                38
  CLUS_2               1                26
  CLUS_3               5                38
D43V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               1                28
  CLUS_3               4                30
  CLUS_4               2                29
D43V7, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               7                35
  CLUS_2               1                22
  CLUS_3               2                43
D43V8, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                11
  CLUS_2               1                24
  CLUS_3               9                65

Clustering(44) Variable = 5p loss mutation analysis
D44V1, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               6                24
  CLUS_2               2                16
  CLUS_3               5                33
  CLUS_4               1                25
D44V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                15
  CLUS_2               1                39
  CLUS_3               1                25
  CLUS_4               9                19
D44V3, multiclass
D44V4, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                11
  CLUS_2               2                20
  CLUS_3               5                29
  CLUS_4               3                 9
D44V5, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                39
  CLUS_2               2                25
  CLUS_3               9                34
D44V6, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               2                27
  CLUS_3               3                31
  CLUS_4               9                22
D44V7, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               9                33
  CLUS_2               1                22
  CLUS_3               4                41
D44V8, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               1                10
  CLUS_2               1                24
  CLUS_3              12                62

Clustering(45) Variable = 5q loss mutation analysis
D45V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               8                22
  CLUS_2               5                13
  CLUS_3               9                29
  CLUS_4               2                24
D45V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               6                34
  CLUS_3               6                20
  CLUS_4              10                18
D45V3, multiclass
D45V4, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                11
  CLUS_2               6                16
  CLUS_3               7                27
  CLUS_4               2                10
D45V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               8                34
  CLUS_2               4                23
  CLUS_3              12                31
D45V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               4                25
  CLUS_3               8                26
  CLUS_4              11                20
D45V7, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              12                30
  CLUS_2               5                18
  CLUS_3               7                38
D45V8, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               2                 9
  CLUS_2               4                21
  CLUS_3              18                56

Clustering(46) Variable = 6p loss mutation analysis
D46V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                28
  CLUS_2               0                18
  CLUS_3               3                35
  CLUS_4               4                22
D46V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               2                38
  CLUS_3               2                24
  CLUS_4               3                25
D46V3, multiclass
D46V4, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                12
  CLUS_2               1                21
  CLUS_3               3                31
  CLUS_4               1                11
D46V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3                39
  CLUS_2               2                25
  CLUS_3               4                39
D46V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               3                26
  CLUS_3               3                31
  CLUS_4               2                29
D46V7, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                40
  CLUS_2               4                19
  CLUS_3               3                42
D46V8, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               3                 8
  CLUS_2               2                23
  CLUS_3               4                70

Clustering(47) Variable = 6q loss mutation analysis
D47V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              15                15
  CLUS_2               5                13
  CLUS_3               4                34
  CLUS_4              16                10
D47V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              10                 8
  CLUS_2               8                32
  CLUS_3               8                18
  CLUS_4              14                14
D47V3, multiclass
D47V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3                 9
  CLUS_2               8                14
  CLUS_3              13                21
  CLUS_4               6                 6
D47V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              14                28
  CLUS_2               5                22
  CLUS_3              21                22
D47V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               5                13
  CLUS_2               7                22
  CLUS_3              11                23
  CLUS_4              17                14
D47V7, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1              17                25
  CLUS_2              12                11
  CLUS_3              11                34
D47V8, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               7                 4
  CLUS_2               7                18
  CLUS_3              26                48

Clustering(48) Variable = 8p loss mutation analysis
D48V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4                26
  CLUS_2               2                16
  CLUS_3               3                35
  CLUS_4               5                21
D48V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               5                13
  CLUS_2               2                38
  CLUS_3               2                24
  CLUS_4               5                23
D48V3, multiclass
D48V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                12
  CLUS_2               4                18
  CLUS_3               6                28
  CLUS_4               2                10
D48V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4                38
  CLUS_2               2                25
  CLUS_3               8                35
D48V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               2                27
  CLUS_3               4                30
  CLUS_4               7                24
D48V7, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1              10                32
  CLUS_2               0                23
  CLUS_3               4                41
D48V8, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                11
  CLUS_2               0                25
  CLUS_3              14                60

Clustering(49) Variable = 8q loss mutation analysis
D49V1, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                29
  CLUS_2               0                18
  CLUS_3               1                37
  CLUS_4               1                25
D49V2, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2                16
  CLUS_2               0                40
  CLUS_3               0                26
  CLUS_4               1                27
D49V3, multiclass
D49V4, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                12
  CLUS_2               1                21
  CLUS_3               2                32
  CLUS_4               0                12
D49V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               2                40
  CLUS_2               0                27
  CLUS_3               1                42
D49V6, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               0                29
  CLUS_3               2                32
  CLUS_4               1                30
D49V7, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3                39
  CLUS_2               0                23
  CLUS_3               0                45
D49V8, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                11
  CLUS_2               0                25
  CLUS_3               3                71

Clustering(50) Variable = 9p loss mutation analysis
D50V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              24                 6
  CLUS_2              13                 5
  CLUS_3              10                28
  CLUS_4              10                16
D50V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              11                 7
  CLUS_2              11                29
  CLUS_3              14                12
  CLUS_4              21                 7
D50V3, multiclass
D50V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               5                 7
  CLUS_2              11                11
  CLUS_3              19                15
  CLUS_4               6                 6
D50V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              26                16
  CLUS_2               6                21
  CLUS_3              25                18
D50V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              12                 6
  CLUS_2              10                19
  CLUS_3              18                16
  CLUS_4              17                14
D50V7, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              26                16
  CLUS_2              14                 9
  CLUS_3              16                29
D50V8, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               6                 5
  CLUS_2               9                16
  CLUS_3              41                33

Clustering(51) Variable = 9q loss mutation analysis
D51V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              18                12
  CLUS_2               6                12
  CLUS_3               9                29
  CLUS_4               9                17
D51V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               5                13
  CLUS_2               9                31
  CLUS_3              12                14
  CLUS_4              16                12
D51V3, multiclass
D51V4, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               4                 8
  CLUS_2              10                12
  CLUS_3              14                20
  CLUS_4               2                10
D51V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              21                21
  CLUS_2               5                22
  CLUS_3              16                27
D51V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              10                 8
  CLUS_2               9                20
  CLUS_3              13                21
  CLUS_4              10                21
D51V7, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1              20                22
  CLUS_2              12                11
  CLUS_3              10                35
D51V8, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               5                 6
  CLUS_2               6                19
  CLUS_3              31                43

Clustering(52) Variable = 10p loss mutation analysis
D52V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               15                 15
  CLUS_2               11                  7
  CLUS_3                8                 30
  CLUS_4               11                 15
D52V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                8                 10
  CLUS_2                9                 31
  CLUS_3               15                 11
  CLUS_4               13                 15
D52V3, multiclass
D52V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                4                  8
  CLUS_2                6                 16
  CLUS_3               19                 15
  CLUS_4                2                 10
D52V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               22                 20
  CLUS_2                3                 24
  CLUS_3               20                 23
D52V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                9                  9
  CLUS_2                4                 25
  CLUS_3               18                 16
  CLUS_4               14                 17
D52V7, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1               25                 17
  CLUS_2               10                 13
  CLUS_3               10                 35
D52V8, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                4                  7
  CLUS_2                6                 19
  CLUS_3               35                 39

Clustering(53) Variable = 10q loss mutation analysis
D53V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               16                 14
  CLUS_2               11                  7
  CLUS_3                9                 29
  CLUS_4               13                 13
D53V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                8                 10
  CLUS_2               10                 30
  CLUS_3               17                  9
  CLUS_4               14                 14
D53V3, multiclass
D53V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                  7
  CLUS_2                8                 14
  CLUS_3               19                 15
  CLUS_4                2                 10
D53V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               23                 19
  CLUS_2                3                 24
  CLUS_3               23                 20
D53V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               12                  6
  CLUS_2                5                 24
  CLUS_3               19                 15
  CLUS_4               13                 18
D53V7, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1               23                 19
  CLUS_2               13                 10
  CLUS_3               13                 32
D53V8, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                6                  5
  CLUS_2                7                 18
  CLUS_3               36                 38

Clustering(54) Variable = 11p loss mutation analysis
D54V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               13                 17
  CLUS_2                7                 11
  CLUS_3                4                 34
  CLUS_4                2                 24
D54V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                7                 11
  CLUS_2                3                 37
  CLUS_3                6                 20
  CLUS_4               10                 18
D54V3, multiclass
D54V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                5                 17
  CLUS_3               11                 23
  CLUS_4                4                  8
D54V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                9                 33
  CLUS_2                2                 25
  CLUS_3               15                 28
D54V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                6                 12
  CLUS_2                3                 26
  CLUS_3                8                 26
  CLUS_4                9                 22
D54V7, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               13                 29
  CLUS_2                6                 17
  CLUS_3                6                 39
D54V8, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                3                  8
  CLUS_2                3                 22
  CLUS_3               19                 55

Clustering(55) Variable = 11q loss mutation analysis
D55V1, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               15                 15
  CLUS_2                8                 10
  CLUS_3                3                 35
  CLUS_4                4                 22
D55V2, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               10                  8
  CLUS_2                4                 36
  CLUS_3                7                 19
  CLUS_4                9                 19
D55V3, multiclass
D55V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 10
  CLUS_2                6                 16
  CLUS_3               13                 21
  CLUS_4                4                  8
D55V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                9                 33
  CLUS_2                3                 24
  CLUS_3               18                 25
D55V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                8                 10
  CLUS_2                2                 27
  CLUS_3                8                 26
  CLUS_4               12                 19
D55V7, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1               13                 29
  CLUS_2                9                 14
  CLUS_3                8                 37
D55V8, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                4                  7
  CLUS_2                3                 22
  CLUS_3               23                 51

Clustering(56) Variable = 12p loss mutation analysis
D56V1, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                3                 27
  CLUS_2                0                 18
  CLUS_3                1                 37
  CLUS_4                1                 25
D56V2, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                 39
  CLUS_3                1                 25
  CLUS_4                2                 26
D56V3, multiclass
D56V4, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 12
  CLUS_2                3                 19
  CLUS_3                2                 32
  CLUS_4                0                 12
D56V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                3                 39
  CLUS_2                1                 26
  CLUS_3                1                 42
D56V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                1                 28
  CLUS_3                2                 32
  CLUS_4                2                 29
D56V7, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 41
  CLUS_2                2                 21
  CLUS_3                2                 43
D56V8, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                1                 24
  CLUS_3                3                 71

Clustering(57) Variable = 12q loss mutation analysis
D57V1, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                5                 25
  CLUS_2                0                 18
  CLUS_3                2                 36
  CLUS_4                1                 25
D57V2, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                 39
  CLUS_3                1                 25
  CLUS_4                5                 23
D57V3, multiclass
D57V4, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                3                 19
  CLUS_3                2                 32
  CLUS_4                1                 11
D57V5, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                4                 38
  CLUS_2                1                 26
  CLUS_3                3                 40
D57V6, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                2                 27
  CLUS_3                3                 31
  CLUS_4                3                 28
D57V7, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                4                 38
  CLUS_2                3                 20
  CLUS_3                1                 44
D57V8, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                1                 24
  CLUS_3                5                 69

Clustering(58) Variable = 13q loss mutation analysis
D58V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                9                 21
  CLUS_2                5                 13
  CLUS_3                2                 36
  CLUS_4                1                 25
D58V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                4                 36
  CLUS_3                4                 22
  CLUS_4                5                 23
D58V3, multiclass
D58V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                3                  9
  CLUS_2                3                 19
  CLUS_3                5                 29
  CLUS_4                1                 11
D58V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                6                 36
  CLUS_2                3                 24
  CLUS_3                8                 35
D58V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                3                 26
  CLUS_3                6                 28
  CLUS_4                5                 26
D58V7, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1               11                 31
  CLUS_2                3                 20
  CLUS_3                3                 42
D58V8, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                3                 22
  CLUS_3               14                 60

Clustering(59) Variable = 14q loss mutation analysis
D59V1, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                8                 22
  CLUS_2                9                  9
  CLUS_3                3                 35
  CLUS_4                5                 21
D59V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                7                 11
  CLUS_2                4                 36
  CLUS_3                8                 18
  CLUS_4                6                 22
D59V3, multiclass
D59V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                2                 10
  CLUS_2                3                 19
  CLUS_3                8                 26
  CLUS_4                4                  8
D59V5, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               12                 30
  CLUS_2                3                 24
  CLUS_3               10                 33
D59V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                5                 24
  CLUS_3               12                 22
  CLUS_4                7                 24
D59V7, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1               11                 31
  CLUS_2                6                 17
  CLUS_3                7                 38
D59V8, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                5                 20
  CLUS_3               18                 56

Clustering(60) Variable = 15q loss mutation analysis
D60V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                 26
  CLUS_2                1                 17
  CLUS_3                0                 38
  CLUS_4                2                 24
D60V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                0                 40
  CLUS_3                2                 24
  CLUS_4                4                 24
D60V3, multiclass
D60V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                1                 21
  CLUS_3                3                 31
  CLUS_4                1                 11
D60V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                4                 38
  CLUS_2                0                 27
  CLUS_3                3                 40
D60V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                 28
  CLUS_3                3                 31
  CLUS_4                2                 29
D60V7, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                3                 39
  CLUS_2                2                 21
  CLUS_3                2                 43
D60V8, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                1                 24
  CLUS_3                5                 69

Clustering(61) Variable = 16p loss mutation analysis
D61V1, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                 28
  CLUS_2                3                 15
  CLUS_3                2                 36
  CLUS_4                1                 25
D61V2, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                 39
  CLUS_3                3                 23
  CLUS_4                3                 25
D61V3, multiclass
D61V4, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 12
  CLUS_2                1                 21
  CLUS_3                4                 30
  CLUS_4                0                 12
D61V5, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                4                 38
  CLUS_2                0                 27
  CLUS_3                4                 39
D61V6, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                1                 28
  CLUS_3                3                 31
  CLUS_4                2                 29
D61V7, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                7                 35
  CLUS_2                1                 22
  CLUS_3                0                 45
D61V8, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                1                 24
  CLUS_3                7                 67

Clustering(62) Variable = 16q loss mutation analysis
D62V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                 25
  CLUS_2                4                 14
  CLUS_3                4                 34
  CLUS_4                3                 23
D62V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                3                 37
  CLUS_3                4                 22
  CLUS_4                7                 21
D62V3, multiclass
D62V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 12
  CLUS_2                2                 20
  CLUS_3                8                 26
  CLUS_4                1                 11
D62V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                 37
  CLUS_2                1                 26
  CLUS_3               10                 33
D62V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                5                 13
  CLUS_2                2                 27
  CLUS_3                4                 30
  CLUS_4                5                 26
D62V7, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1               11                 31
  CLUS_2                3                 20
  CLUS_3                2                 43
D62V8, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                1                 24
  CLUS_3               14                 60

Clustering(63) Variable = 17p loss mutation analysis
D63V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               11                 19
  CLUS_2                5                 13
  CLUS_3                7                 31
  CLUS_4                5                 21
D63V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                4                 36
  CLUS_3                4                 22
  CLUS_4               16                 12
D63V3, multiclass
D63V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 10
  CLUS_2                6                 16
  CLUS_3               10                 24
  CLUS_4                2                 10
D63V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                8                 34
  CLUS_2                4                 23
  CLUS_3               16                 27
D63V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                7                 11
  CLUS_2                5                 24
  CLUS_3                4                 30
  CLUS_4               12                 19
D63V7, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               15                 27
  CLUS_2                4                 19
  CLUS_3                8                 37
D63V8, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                4                 21
  CLUS_3               22                 52

Clustering(64) Variable = 17q loss mutation analysis
D64V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 28
  CLUS_2                4                 14
  CLUS_3                5                 33
  CLUS_4                2                 24
D64V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                3                 37
  CLUS_3                2                 24
  CLUS_4                5                 23
D64V3, multiclass
D64V4, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 12
  CLUS_2                3                 19
  CLUS_3                5                 29
  CLUS_4                1                 11
D64V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                4                 38
  CLUS_2                1                 26
  CLUS_3                8                 35
D64V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                2                 27
  CLUS_3                3                 31
  CLUS_4                6                 25
D64V7, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                5                 37
  CLUS_2                2                 21
  CLUS_3                5                 40
D64V8, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                2                 23
  CLUS_3               10                 64

Clustering(65) Variable = 18p loss mutation analysis
D65V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                6                 24
  CLUS_2                5                 13
  CLUS_3                5                 33
  CLUS_4                2                 24
D65V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                5                 13
  CLUS_2                1                 39
  CLUS_3                8                 18
  CLUS_4                4                 24
D65V3, multiclass
D65V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                2                 10
  CLUS_2                1                 21
  CLUS_3                6                 28
  CLUS_4                1                 11
D65V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               13                 29
  CLUS_2                1                 26
  CLUS_3                4                 39
D65V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                2                 27
  CLUS_3               11                 23
  CLUS_4                2                 29
D65V7, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               12                 30
  CLUS_2                2                 21
  CLUS_3                4                 41
D65V8, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                3                 22
  CLUS_3               14                 60

Clustering(66) Variable = 18q loss mutation analysis
D66V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                4                 26
  CLUS_2                5                 13
  CLUS_3                4                 34
  CLUS_4                5                 21
D66V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                4                 14
  CLUS_2                1                 39
  CLUS_3                9                 17
  CLUS_4                4                 24
D66V3, multiclass
D66V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                2                 10
  CLUS_2                0                 22
  CLUS_3                7                 27
  CLUS_4                1                 11
D66V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               11                 31
  CLUS_2                1                 26
  CLUS_3                6                 37
D66V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                5                 13
  CLUS_2                2                 27
  CLUS_3                9                 25
  CLUS_4                2                 29
D66V7, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               11                 31
  CLUS_2                3                 20
  CLUS_3                4                 41
D66V8, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                4                 21
  CLUS_3               13                 61

Clustering(67) Variable = 19p loss mutation analysis
D67V1, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                 26
  CLUS_2                1                 17
  CLUS_3                3                 35
  CLUS_4                4                 22
D67V2, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                6                 34
  CLUS_3                2                 24
  CLUS_4                3                 25
D67V3, multiclass
D67V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                1                 21
  CLUS_3                4                 30
  CLUS_4                2                 10
D67V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                4                 38
  CLUS_2                1                 26
  CLUS_3                7                 36
D67V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                6                 12
  CLUS_2                2                 27
  CLUS_3                3                 31
  CLUS_4                1                 30
D67V7, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                8                 34
  CLUS_2                3                 20
  CLUS_3                1                 44
D67V8, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                1                 24
  CLUS_3                9                 65

Clustering(68) Variable = 19q loss mutation analysis
D68V1, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                6                 24
  CLUS_2                0                 18
  CLUS_3                2                 36
  CLUS_4                4                 22
D68V2, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                4                 36
  CLUS_3                2                 24
  CLUS_4                5                 23
D68V3, multiclass
D68V4, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                3                 19
  CLUS_3                4                 30
  CLUS_4                0                 12
D68V5, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                3                 39
  CLUS_2                1                 26
  CLUS_3                8                 35
D68V6, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                5                 13
  CLUS_2                2                 27
  CLUS_3                1                 33
  CLUS_4                4                 27
D68V7, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                7                 35
  CLUS_2                3                 20
  CLUS_3                2                 43
D68V8, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                1                 10
  CLUS_2                1                 24
  CLUS_3               10                 64

Clustering(69) Variable = 20p loss mutation analysis
D69V1, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                 29
  CLUS_2                1                 17
  CLUS_3                0                 38
  CLUS_4                1                 25
D69V2, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                 17
  CLUS_2                1                 39
  CLUS_3                1                 25
  CLUS_4                0                 28
D69V3, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 78 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2JD         TCGA-D3-A3CE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D9-A148         TCGA-D9-A1JW         TCGA-D9-A1JX 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1IB         TCGA-EE-A17X         TCGA-EE-A181 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29N 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29R         TCGA-EE-A29S 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A0         TCGA-EE-A2A2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GC         TCGA-EE-A2GH 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2GI         TCGA-EE-A2GK         TCGA-EE-A2GL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2GS         TCGA-EE-A2GT         TCGA-EE-A2GU 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2MC         TCGA-EE-A2MD         TCGA-EE-A2MI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2MJ         TCGA-EE-A2MK         TCGA-EE-A2ML 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2MM         TCGA-EE-A2MN         TCGA-EE-A2MP 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2MR         TCGA-EE-A2MS         TCGA-EE-A2MT 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A3AA         TCGA-EE-A3AB         TCGA-EE-A3AC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A3AD         TCGA-EE-A3AE         TCGA-EE-A3AF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-ER-A19J         TCGA-ER-A19L 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A19O         TCGA-ER-A1A1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1YW         TCGA-FS-A1Z4         TCGA-FS-A1ZD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZG         TCGA-FS-A1ZH         TCGA-FS-A1ZJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-GN-A264         TCGA-GN-A265 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D69V4, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 78 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q8         TCGA-D3-A1Q9         TCGA-D3-A2J6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2J8         TCGA-D3-A2JD         TCGA-D3-A3CE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D9-A148         TCGA-D9-A1JW         TCGA-D9-A1JX 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1IB         TCGA-EE-A17X         TCGA-EE-A181 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20F         TCGA-EE-A29C 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29L         TCGA-EE-A29N 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29R         TCGA-EE-A29S 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A0         TCGA-EE-A2A2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-EE-A2GC         TCGA-EE-A2GH 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2GI         TCGA-EE-A2GK         TCGA-EE-A2GL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2GS         TCGA-EE-A2GT         TCGA-EE-A2GU 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2M5         TCGA-EE-A2M6         TCGA-EE-A2M8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2MC         TCGA-EE-A2MD         TCGA-EE-A2MI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2MJ         TCGA-EE-A2MK         TCGA-EE-A2ML 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2MM         TCGA-EE-A2MN         TCGA-EE-A2MP 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2MR         TCGA-EE-A2MS         TCGA-EE-A2MT 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A3AA         TCGA-EE-A3AB         TCGA-EE-A3AC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A3AD         TCGA-EE-A3AE         TCGA-EE-A3AF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-ER-A19J         TCGA-ER-A19L 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A19O         TCGA-ER-A1A1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1YW         TCGA-FS-A1Z4         TCGA-FS-A1ZD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZG         TCGA-FS-A1ZH         TCGA-FS-A1ZJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-GN-A264         TCGA-GN-A265 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D69V5, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                0                 42
  CLUS_2                2                 25
  CLUS_3                1                 42
D69V6, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                2                 27
  CLUS_3                0                 34
  CLUS_4                1                 30
D69V7, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                3                 39
  CLUS_2                0                 23
  CLUS_3                0                 45
D69V8, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                0                 25
  CLUS_3                3                 71

Clustering(70) Variable = 21q loss mutation analysis
D70V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                 26
  CLUS_2                3                 15
  CLUS_3                3                 35
  CLUS_4                5                 21
D70V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                2                 38
  CLUS_3                5                 21
  CLUS_4                6                 22
D70V3, multiclass
D70V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                3                 19
  CLUS_3                8                 26
  CLUS_4                1                 11
D70V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                7                 35
  CLUS_2                2                 25
  CLUS_3                6                 37
D70V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 15
  CLUS_2                3                 26
  CLUS_3                5                 29
  CLUS_4                4                 27
D70V7, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               11                 31
  CLUS_2                3                 20
  CLUS_3                1                 44
D70V8, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                  9
  CLUS_2                2                 23
  CLUS_3               11                 63

Clustering(71) Variable = 22q loss mutation analysis
D71V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2                2                 16
  CLUS_3                2                 36
  CLUS_4                3                 23
D71V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                 16
  CLUS_2                2                 38
  CLUS_3                2                 24
  CLUS_4                1                 27
D71V3, multiclass
D71V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                1                 11
  CLUS_2                2                 20
  CLUS_3                3                 31
  CLUS_4                1                 11
D71V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                4                 38
  CLUS_2                0                 27
  CLUS_3                3                 40
D71V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                 18
  CLUS_2                2                 27
  CLUS_3                3                 31
  CLUS_4                2                 29
D71V7, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                5                 37
  CLUS_2                1                 22
  CLUS_3                1                 44
D71V8, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                 11
  CLUS_2                1                 24
  CLUS_3                6                 68

Clustering(72) Variable = Xq loss mutation analysis
D72V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                29
  CLUS_2               0                18
  CLUS_3               0                38
  CLUS_4               2                24
D72V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                17
  CLUS_2               0                40
  CLUS_3               1                25
  CLUS_4               1                27
D72V3, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                78 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2JD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D9-A148        TCGA-D9-A1JW        TCGA-D9-A1JX 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-EE-A17X        TCGA-EE-A181        TCGA-EE-A185 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29R        TCGA-EE-A29S 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A0        TCGA-EE-A2A2        TCGA-EE-A2A6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2GC        TCGA-EE-A2GH        TCGA-EE-A2GI        TCGA-EE-A2GK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2GL        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2GU 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2M5        TCGA-EE-A2M6        TCGA-EE-A2M8        TCGA-EE-A2MC 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2MD        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2ML        TCGA-EE-A2MM        TCGA-EE-A2MN        TCGA-EE-A2MP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2MR        TCGA-EE-A2MS        TCGA-EE-A2MT        TCGA-EE-A3AA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AC        TCGA-EE-A3AD        TCGA-EE-A3AE 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A3AF        TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A19O        TCGA-ER-A1A1        TCGA-FS-A1YW 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A1Z4        TCGA-FS-A1ZD        TCGA-FS-A1ZG        TCGA-FS-A1ZH 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A1ZP        TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A267 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D72V4, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                78 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q7        TCGA-D3-A1Q8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2JD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D9-A148        TCGA-D9-A1JW        TCGA-D9-A1JX 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-EE-A17X        TCGA-EE-A181        TCGA-EE-A185 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29R        TCGA-EE-A29S 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A0        TCGA-EE-A2A2        TCGA-EE-A2A6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2GC        TCGA-EE-A2GH        TCGA-EE-A2GI        TCGA-EE-A2GK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2GL        TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2GU 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2M5        TCGA-EE-A2M6        TCGA-EE-A2M8        TCGA-EE-A2MC 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2MD        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2ML        TCGA-EE-A2MM        TCGA-EE-A2MN        TCGA-EE-A2MP 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2MR        TCGA-EE-A2MS        TCGA-EE-A2MT        TCGA-EE-A3AA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A3AB        TCGA-EE-A3AC        TCGA-EE-A3AD        TCGA-EE-A3AE 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A3AF        TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19N        TCGA-ER-A19O        TCGA-ER-A1A1        TCGA-FS-A1YW 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A1Z4        TCGA-FS-A1ZD        TCGA-FS-A1ZG        TCGA-FS-A1ZH 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A1ZP        TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A267 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D72V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                41
  CLUS_2               0                27
  CLUS_3               2                41
D72V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                18
  CLUS_2               0                29
  CLUS_3               1                33
  CLUS_4               2                29
D72V7, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2                40
  CLUS_2               0                23
  CLUS_3               1                44
D72V8, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                11
  CLUS_2               0                25
  CLUS_3               3                71
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"             "RPPA_CNMF" 
                     V4                      V5                      V6 
   "RPPA_CHIERARCHICAL"          "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL" 
                     V7                      V8 
          "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
