
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/335597/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/STAD-TP/2667074/1.GDAC_mergedClustering.Finished/STAD-TP.transferedmergedcluster.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=STAD-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=STAD-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=257, in cluster file=237, common to both=237
[1] "Reduce the number of clustering variables from 80 to 74."
[1]  74 237
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                9               228 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                9               228 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               30               207 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               30               207 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               13               224 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               13               224 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               14               223 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               14               223 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5               232 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5               232 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               17               220 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               17               220 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               233 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               233 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               30               207 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               30               207 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6               231 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6               231 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               15               222 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               15               222 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               13               224 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               13               224 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               64               173 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               64               173 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               56               181 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               56               181 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               61               176 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               61               176 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               84               153 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               84               153 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               13               224 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               13               224 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               17               220 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               17               220 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                29                208 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                29                208 
[1] "10q gain mutation analysis"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                17                220 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                17                220 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 7                230 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 7                230 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                12                225 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                12                225 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                20                217 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                20                217 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                222 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                15                222 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                42                195 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                42                195 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 9                228 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 9                228 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                13                224 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                13                224 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                227 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                227 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                229 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                229 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                11                226 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                11                226 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                16                221 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                16                221 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                229 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                229 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                10                227 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                10                227 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                21                216 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                21                216 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                91                146 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                91                146 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               115                122 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               115                122 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                233 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                233 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                9               228 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                9               228 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4               233 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4               233 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5               232 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5               232 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               16               221 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               16               221 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9               228 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9               228 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               38               199 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               38               199 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               34               203 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               34               203 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               13               224 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               13               224 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               25               212 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               25               212 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               10               227 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               10               227 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               16               221 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               16               221 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4               233 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4               233 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                9               228 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                9               228 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               17               220 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               17               220 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5               232 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5               232 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               38               199 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               38               199 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               20               217 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               20               217 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                14                223 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                14                223 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                14                223 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                14                223 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                15                222 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                15                222 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                11                226 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                11                226 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                15                222 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                15                222 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                229 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                229 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 8                229 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 8                229 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                19                218 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                19                218 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                15                222 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                15                222 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                226 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                226 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                17                220 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                17                220 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                46                191 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                46                191 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                15                222 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                15                222 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                24                213 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                24                213 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                37                200 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                37                200 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                23                214 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                23                214 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                16                221 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                16                221 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                230 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                230 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                42                195 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                42                195 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                30                207 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                30                207 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               12               225 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               12               225 
[1] "data2feature, selection=ALL"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 6 rows and 237 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 237 columns, 0 survival variables, and 6 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               3                27
  CLUS_2               6                93
  CLUS_3               0               108
D1V2, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               3                49
  CLUS_3               2                53
  CLUS_4               0                55
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2    1
  1P GAIN WILD-TYPE   20   20
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               2                20
  CLUS_2               1                20
D1V4, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               0                15
  CLUS_2               1                 6
  CLUS_3               2                19
D1V5, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               5                84
  CLUS_2               1                54
  CLUS_3               3                89
D1V6, multiclass
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  CLUS_1               1                58
  CLUS_2               5                99
  CLUS_3               3                70

Clustering(2) Variable = 1q gain mutation analysis
D2V1, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               6                24
  CLUS_2              21                78
  CLUS_3               3               105
D2V2, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               8                44
  CLUS_3               4                51
  CLUS_4              12                43
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3    2
  1Q GAIN WILD-TYPE   19   19
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               3                19
  CLUS_2               2                19
D2V4, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               1                14
  CLUS_2               1                 6
  CLUS_3               3                18
D2V5, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1               9                80
  CLUS_2               2                53
  CLUS_3              19                73
D2V6, multiclass
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CLUS_1              13                46
  CLUS_2              12                92
  CLUS_3               5                68

Clustering(3) Variable = 2p gain mutation analysis
D3V1, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               0                30
  CLUS_2              12                87
  CLUS_3               1               107
D3V2, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               1                51
  CLUS_3               1                54
  CLUS_4               8                47
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2    0
  2P GAIN WILD-TYPE   20   21
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               2                20
  CLUS_2               0                21
D3V4, multiclass
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                41 
       TCGA-BR-4187        TCGA-BR-4191        TCGA-BR-4201        TCGA-BR-4253 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257        TCGA-BR-4267 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362        TCGA-BR-4363 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-4369 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-4370        TCGA-BR-4371        TCGA-CG-4301        TCGA-CG-4304 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4438 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4444 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4477 
"2P GAIN WILD-TYPE" 
D3V5, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               4                85
  CLUS_2               1                54
  CLUS_3               8                84
D3V6, multiclass
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  CLUS_1               8                51
  CLUS_2               2               102
  CLUS_3               3                70

Clustering(4) Variable = 2q gain mutation analysis
D4V1, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                30
  CLUS_2              13                86
  CLUS_3               1               107
D4V2, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               2                50
  CLUS_3               0                55
  CLUS_4               8                47
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3    0
  2Q GAIN WILD-TYPE   19   21
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               3                19
  CLUS_2               0                21
D4V4, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               0                15
  CLUS_2               0                 7
  CLUS_3               3                18
D4V5, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               4                85
  CLUS_2               2                53
  CLUS_3               8                84
D4V6, multiclass
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CLUS_1               7                52
  CLUS_2               3               101
  CLUS_3               4                69

Clustering(5) Variable = 3p gain mutation analysis
D5V1, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                30
  CLUS_2               3                96
  CLUS_3               2               106
D5V2, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                27
  CLUS_2               0                52
  CLUS_3               1                54
  CLUS_4               2                53
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2    0
  3P GAIN WILD-TYPE   20   21
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               2                20
  CLUS_2               0                21
D5V4, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                41 
       TCGA-BR-4187        TCGA-BR-4191        TCGA-BR-4201        TCGA-BR-4253 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257        TCGA-BR-4279 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294        TCGA-BR-4357 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-4361        TCGA-BR-4362        TCGA-BR-4363        TCGA-BR-4366 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-4367        TCGA-BR-4369        TCGA-BR-4370        TCGA-BR-4371 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4442 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4460 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4477 
"3P GAIN WILD-TYPE" 
D5V5, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               4                85
  CLUS_2               0                55
  CLUS_3               1                91
D5V6, multiclass
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  CLUS_1               0                59
  CLUS_2               4               100
  CLUS_3               1                72

Clustering(6) Variable = 3q gain mutation analysis
D6V1, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               2                28
  CLUS_2              11                88
  CLUS_3               4               104
D6V2, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               3                24
  CLUS_2               1                51
  CLUS_3               2                53
  CLUS_4               5                50
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      6    0
  3Q GAIN WILD-TYPE   16   21
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               6                16
  CLUS_2               0                21
D6V4, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               0                15
  CLUS_2               1                 6
  CLUS_3               5                16
D6V5, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               9                80
  CLUS_2               3                52
  CLUS_3               5                87
D6V6, multiclass
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CLUS_1               4                55
  CLUS_2              11                93
  CLUS_3               2                71

Clustering(7) Variable = 4p gain mutation analysis
D7V1, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                29
  CLUS_2               3                96
  CLUS_3               0               108
D7V2, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               187 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6453 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707        TCGA-BR-7715 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7723 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7958 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7959        TCGA-BR-8058        TCGA-BR-8059        TCGA-BR-8060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8360        TCGA-BR-8361        TCGA-BR-8362        TCGA-BR-8363 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8364        TCGA-BR-8365        TCGA-BR-8366        TCGA-BR-8367 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8368        TCGA-BR-8369        TCGA-BR-8370        TCGA-BR-8371 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8372        TCGA-BR-8373        TCGA-BR-8380        TCGA-BR-8381 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8382        TCGA-BR-8384        TCGA-BR-8483        TCGA-BR-8485 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8486        TCGA-BR-8487        TCGA-BR-8588        TCGA-BR-8589 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8590        TCGA-BR-8591        TCGA-BR-8592        TCGA-BR-8676 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8677        TCGA-BR-8678        TCGA-BR-8679        TCGA-BR-8680 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8682        TCGA-BR-8683        TCGA-BR-8686        TCGA-BR-8687 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8690        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-8524        TCGA-CD-8525        TCGA-CD-8526        TCGA-CD-8527 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-8528        TCGA-CD-8529        TCGA-CD-8530        TCGA-CD-8531 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-8532        TCGA-CD-8533        TCGA-CD-8534        TCGA-CD-8535 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-8536        TCGA-CG-4437        TCGA-CG-4441        TCGA-CG-5716 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-6518        TCGA-D7-6519 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6822        TCGA-D7-8570        TCGA-D7-8572        TCGA-D7-8573 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-8574        TCGA-D7-8575        TCGA-D7-8576        TCGA-D7-8578 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-8579        TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-8210        TCGA-FP-8211        TCGA-FP-8631        TCGA-HF-7131 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-HU-8238        TCGA-HU-8243        TCGA-HU-8244 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HU-8245        TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HU-8608        TCGA-HU-8610        TCGA-IN-7806        TCGA-IN-7808 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IN-8462        TCGA-IN-8663        TCGA-IP-7968 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    1
  4P GAIN WILD-TYPE   21   20
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               1                21
  CLUS_2               1                20
D7V4, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                41 
       TCGA-BR-4187        TCGA-BR-4191        TCGA-BR-4201        TCGA-BR-4253 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257        TCGA-BR-4267 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362        TCGA-BR-4363 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-4369 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4370        TCGA-BR-4371        TCGA-CG-4301        TCGA-CG-4304 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4438 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4442        TCGA-CG-4444        TCGA-CG-4449 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4476 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4477 
"4P GAIN WILD-TYPE" 
D7V5, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               2                87
  CLUS_2               1                54
  CLUS_3               1                91
D7V6, multiclass
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  CLUS_1               0                59
  CLUS_2               2               102
  CLUS_3               2                71

Clustering(8) Variable = 5p gain mutation analysis
D8V1, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                28
  CLUS_2              24                75
  CLUS_3               4               104
D8V2, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               2                25
  CLUS_2               3                49
  CLUS_3               4                51
  CLUS_4              11                44
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3    6
  5P GAIN WILD-TYPE   19   15
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               3                19
  CLUS_2               6                15
D8V4, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1               5                10
  CLUS_2               1                 6
  CLUS_3               3                18
D8V5, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              11                78
  CLUS_2               3                52
  CLUS_3              16                76
D8V6, multiclass
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  CLUS_1              12                47
  CLUS_2              12                92
  CLUS_3               6                67

Clustering(9) Variable = 5q gain mutation analysis
D9V1, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               1                29
  CLUS_2               5                94
  CLUS_3               0               108
D9V2, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2               187 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6453 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707        TCGA-BR-7716 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7958        TCGA-BR-7959 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8058        TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        TCGA-BR-8360 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8361        TCGA-BR-8362        TCGA-BR-8363        TCGA-BR-8364 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8365        TCGA-BR-8366        TCGA-BR-8367        TCGA-BR-8368 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8369        TCGA-BR-8370        TCGA-BR-8371        TCGA-BR-8372 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8373        TCGA-BR-8380        TCGA-BR-8381        TCGA-BR-8382 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8384        TCGA-BR-8483        TCGA-BR-8484        TCGA-BR-8485 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8486        TCGA-BR-8487        TCGA-BR-8588        TCGA-BR-8589 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8590        TCGA-BR-8591        TCGA-BR-8592        TCGA-BR-8676 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8677        TCGA-BR-8678        TCGA-BR-8679        TCGA-BR-8680 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8682        TCGA-BR-8683        TCGA-BR-8686        TCGA-BR-8687 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8690        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-8524        TCGA-CD-8525        TCGA-CD-8526        TCGA-CD-8527 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-8528        TCGA-CD-8529        TCGA-CD-8530        TCGA-CD-8531 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-8532        TCGA-CD-8533        TCGA-CD-8534        TCGA-CD-8535 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-8536        TCGA-CG-4437        TCGA-CG-4441        TCGA-CG-5716 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-D7-8570        TCGA-D7-8572 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-8573        TCGA-D7-8574        TCGA-D7-8575        TCGA-D7-8576 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-8578        TCGA-D7-8579        TCGA-EQ-5647        TCGA-EQ-8122 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FP-8210        TCGA-FP-8211        TCGA-FP-8631        TCGA-HF-7131 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HJ-7597        TCGA-HU-8238        TCGA-HU-8243        TCGA-HU-8244 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HU-8245        TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HU-8608        TCGA-HU-8610        TCGA-IN-7806        TCGA-IN-7808 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-IN-8462        TCGA-IN-8663        TCGA-IP-7968 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    3
  5Q GAIN WILD-TYPE   22   18
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               0                22
  CLUS_2               3                18
D9V4, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               3                12
  CLUS_2               0                 7
  CLUS_3               0                21
D9V5, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                87
  CLUS_2               0                55
  CLUS_3               4                88
D9V6, multiclass
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CLUS_1               2                57
  CLUS_2               3               101
  CLUS_3               1                72

Clustering(10) Variable = 6p gain mutation analysis
D10V1, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                28
  CLUS_2              12                87
  CLUS_3               1               107
D10V2, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               3                49
  CLUS_3               0                55
  CLUS_4               6                49
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    2
  6P GAIN WILD-TYPE   20   19
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               2                20
  CLUS_2               2                19
D10V4, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               1                14
  CLUS_2               1                 6
  CLUS_3               2                19
D10V5, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               3                86
  CLUS_2               1                54
  CLUS_3              11                81
D10V6, multiclass
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  CLUS_1               6                53
  CLUS_2               4               100
  CLUS_3               5                68

Clustering(11) Variable = 6q gain mutation analysis
D11V1, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                29
  CLUS_2              11                88
  CLUS_3               1               107
D11V2, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               0                27
  CLUS_2               3                49
  CLUS_3               0                55
  CLUS_4               6                49
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    2
  6Q GAIN WILD-TYPE   21   19
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                21
  CLUS_2               2                19
D11V4, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               1                14
  CLUS_2               1                 6
  CLUS_3               1                20
D11V5, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               3                86
  CLUS_2               1                54
  CLUS_3               9                83
D11V6, multiclass
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CLUS_1               5                54
  CLUS_2               3               101
  CLUS_3               5                68

Clustering(12) Variable = 7p gain mutation analysis
D12V1, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              10                20
  CLUS_2              44                55
  CLUS_3              10                98
D12V2, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               3                24
  CLUS_2              16                36
  CLUS_3               8                47
  CLUS_4              21                34
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8    7
  7P GAIN WILD-TYPE   14   14
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               8                14
  CLUS_2               7                14
D12V4, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1               6                 9
  CLUS_2               1                 6
  CLUS_3               8                13
D12V5, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              26                63
  CLUS_2               7                48
  CLUS_3              31                61
D12V6, multiclass
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  CLUS_1              24                35
  CLUS_2              27                77
  CLUS_3              13                60

Clustering(13) Variable = 7q gain mutation analysis
D13V1, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              10                20
  CLUS_2              37                62
  CLUS_3               9                99
D13V2, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               3                24
  CLUS_2              13                39
  CLUS_3               6                49
  CLUS_4              17                38
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8    8
  7Q GAIN WILD-TYPE   14   13
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               8                14
  CLUS_2               8                13
D13V4, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1               6                 9
  CLUS_2               2                 5
  CLUS_3               8                13
D13V5, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              28                61
  CLUS_2               6                49
  CLUS_3              22                70
D13V6, multiclass
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CLUS_1              17                42
  CLUS_2              26                78
  CLUS_3              13                60

Clustering(14) Variable = 8p gain mutation analysis
D14V1, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              26                 4
  CLUS_2              26                73
  CLUS_3               9                99
D14V2, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               6                21
  CLUS_2              14                38
  CLUS_3               5                50
  CLUS_4              16                39
D14V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      8   10
  8P GAIN WILD-TYPE   14   11
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               8                14
  CLUS_2              10                11
D14V4, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1               7                 8
  CLUS_2               2                 5
  CLUS_3               9                12
D14V5, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              29                60
  CLUS_2               6                49
  CLUS_3              26                66
D14V6, multiclass
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  CLUS_1              15                44
  CLUS_2              30                74
  CLUS_3              16                57

Clustering(15) Variable = 8q gain mutation analysis
D15V1, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              26                 4
  CLUS_2              45                54
  CLUS_3              13                95
D15V2, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               6                21
  CLUS_2              18                34
  CLUS_3               7                48
  CLUS_4              28                27
D15V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     10   13
  8Q GAIN WILD-TYPE   12    8
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              10                12
  CLUS_2              13                 8
D15V4, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1               9                 6
  CLUS_2               4                 3
  CLUS_3              10                11
D15V5, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              38                51
  CLUS_2              10                45
  CLUS_3              36                56
D15V6, multiclass
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CLUS_1              25                34
  CLUS_2              40                64
  CLUS_3              19                54

Clustering(16) Variable = 9p gain mutation analysis
D16V1, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4                26
  CLUS_2               7                92
  CLUS_3               2               106
D16V2, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               5                47
  CLUS_3               2                53
  CLUS_4               2                53
D16V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0    3
  9P GAIN WILD-TYPE   22   18
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               0                22
  CLUS_2               3                18
D16V4, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               2                13
  CLUS_2               1                 6
  CLUS_3               0                21
D16V5, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               6                83
  CLUS_2               3                52
  CLUS_3               4                88
D16V6, multiclass
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  CLUS_1               4                55
  CLUS_2               7                97
  CLUS_3               2                71

Clustering(17) Variable = 9q gain mutation analysis
D17V1, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               4                26
  CLUS_2              11                88
  CLUS_3               2               106
D17V2, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               1                26
  CLUS_2               4                48
  CLUS_3               4                51
  CLUS_4               4                51
D17V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    4
  9Q GAIN WILD-TYPE   22   17
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               0                22
  CLUS_2               4                17
D17V4, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               2                13
  CLUS_2               2                 5
  CLUS_3               0                21
D17V5, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               8                81
  CLUS_2               3                52
  CLUS_3               6                86
D17V6, multiclass
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CLUS_1               3                56
  CLUS_2              10                94
  CLUS_3               4                69

Clustering(18) Variable = 10p gain mutation analysis
D18V1, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 29
  CLUS_2               25                 74
  CLUS_3                3                105
D18V2, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                4                 48
  CLUS_3                3                 52
  CLUS_4               13                 42
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5    2
  10P GAIN WILD-TYPE   17   19
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                5                 17
  CLUS_2                2                 19
D18V4, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                0                  7
  CLUS_3                5                 16
D18V5, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1                9                 80
  CLUS_2                6                 49
  CLUS_3               14                 78
D18V6, multiclass
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  CLUS_1               12                 47
  CLUS_2                8                 96
  CLUS_3                9                 64

Clustering(19) Variable = 10q gain mutation analysis
D19V1, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 29
  CLUS_2               13                 86
  CLUS_3                3                105
D19V2, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                4                 48
  CLUS_3                1                 54
  CLUS_4                8                 47
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    0
  10Q GAIN WILD-TYPE   19   21
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                3                 19
  CLUS_2                0                 21
D19V4, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                0                 15
  CLUS_2                0                  7
  CLUS_3                3                 18
D19V5, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                2                 87
  CLUS_2                4                 51
  CLUS_3               11                 81
D19V6, multiclass
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CLUS_1                6                 53
  CLUS_2                6                 98
  CLUS_3                5                 68

Clustering(20) Variable = 11p gain mutation analysis
D20V1, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 29
  CLUS_2                5                 94
  CLUS_3                1                107
D20V2, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                2                 50
  CLUS_3                0                 55
  CLUS_4                2                 53
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    0
  11P GAIN WILD-TYPE   21   21
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                1                 21
  CLUS_2                0                 21
D20V4, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 42 
        TCGA-BR-4187         TCGA-BR-4191         TCGA-BR-4201 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-4253         TCGA-BR-4255         TCGA-BR-4256 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-4257         TCGA-BR-4267         TCGA-BR-4279 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-4280         TCGA-BR-4292         TCGA-BR-4294 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-4357         TCGA-BR-4361         TCGA-BR-4362 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-4363         TCGA-BR-4366         TCGA-BR-4367 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-4369         TCGA-BR-4370         TCGA-BR-4371 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4438 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4442         TCGA-CG-4443 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4460 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4475         TCGA-CG-4476         TCGA-CG-4477 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D20V5, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                2                 87
  CLUS_2                1                 54
  CLUS_3                4                 88
D20V6, multiclass
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  CLUS_1                3                 56
  CLUS_2                2                102
  CLUS_3                2                 71

Clustering(21) Variable = 11q gain mutation analysis
D21V1, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                1                 29
  CLUS_2                9                 90
  CLUS_3                2                106
D21V2, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                3                 49
  CLUS_3                0                 55
  CLUS_4                4                 51
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    0
  11Q GAIN WILD-TYPE   20   21
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                0                 21
D21V4, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 41 
        TCGA-BR-4187         TCGA-BR-4191         TCGA-BR-4201 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-4253         TCGA-BR-4255         TCGA-BR-4256 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-4257         TCGA-BR-4267         TCGA-BR-4279 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-4280         TCGA-BR-4292         TCGA-BR-4294 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-4357         TCGA-BR-4361         TCGA-BR-4362 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-4363         TCGA-BR-4366         TCGA-BR-4367 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-4369         TCGA-BR-4370         TCGA-BR-4371 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4438 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4442         TCGA-CG-4443 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4460 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4474         TCGA-CG-4475 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4476         TCGA-CG-4477 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D21V5, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                3                 86
  CLUS_2                2                 53
  CLUS_3                7                 85
D21V6, multiclass
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CLUS_1                4                 55
  CLUS_2                5                 99
  CLUS_3                3                 70

Clustering(22) Variable = 12p gain mutation analysis
D22V1, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               17                 82
  CLUS_3                3                105
D22V2, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                3                 49
  CLUS_3                5                 50
  CLUS_4                9                 46
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3    0
  12P GAIN WILD-TYPE   19   21
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                3                 19
  CLUS_2                0                 21
D22V4, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                0                 15
  CLUS_2                0                  7
  CLUS_3                3                 18
D22V5, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                9                 80
  CLUS_2                1                 54
  CLUS_3               10                 82
D22V6, multiclass
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  CLUS_1                6                 53
  CLUS_2                9                 95
  CLUS_3                5                 68

Clustering(23) Variable = 12q gain mutation analysis
D23V1, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               12                 87
  CLUS_3                3                105
D23V2, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                1                 51
  CLUS_3                3                 52
  CLUS_4                6                 49
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4    0
  12Q GAIN WILD-TYPE   18   21
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                4                 18
  CLUS_2                0                 21
D23V4, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                0                 15
  CLUS_2                1                  6
  CLUS_3                3                 18
D23V5, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                5                 84
  CLUS_2                2                 53
  CLUS_3                8                 84
D23V6, multiclass
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CLUS_1                5                 54
  CLUS_2                7                 97
  CLUS_3                3                 70

Clustering(24) Variable = 13q gain mutation analysis
D24V1, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                6                 24
  CLUS_2               29                 70
  CLUS_3                7                101
D24V2, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                3                 24
  CLUS_2                7                 45
  CLUS_3                4                 51
  CLUS_4               18                 37
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    5
  13Q GAIN WILD-TYPE   18   16
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                4                 18
  CLUS_2                5                 16
D24V4, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1                4                 11
  CLUS_2                1                  6
  CLUS_3                4                 17
D24V5, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               16                 73
  CLUS_2                7                 48
  CLUS_3               19                 73
D24V6, multiclass
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CLUS_1               15                 44
  CLUS_2               15                 89
  CLUS_3               12                 61

Clustering(25) Variable = 15q gain mutation analysis
D25V1, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                 30
  CLUS_2                9                 90
  CLUS_3                0                108
D25V2, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                2                 50
  CLUS_3                2                 53
  CLUS_4                5                 50
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    0
  15Q GAIN WILD-TYPE   22   21
D25V4, multiclass
D25V5, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                4                 85
  CLUS_2                1                 54
  CLUS_3                4                 88
D25V6, multiclass
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CLUS_1                5                 54
  CLUS_2                4                100
  CLUS_3                0                 73

Clustering(26) Variable = 16p gain mutation analysis
D26V1, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               11                 88
  CLUS_3                2                106
D26V2, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                0                 52
  CLUS_3                4                 51
  CLUS_4                5                 50
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3    1
  16P GAIN WILD-TYPE   19   20
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                3                 19
  CLUS_2                1                 20
D26V4, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                0                  7
  CLUS_3                3                 18
D26V5, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                4                 85
  CLUS_2                2                 53
  CLUS_3                7                 85
D26V6, multiclass
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  CLUS_1                5                 54
  CLUS_2                3                101
  CLUS_3                5                 68

Clustering(27) Variable = 16q gain mutation analysis
D27V1, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                 30
  CLUS_2                9                 90
  CLUS_3                1                107
D27V2, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                2                 50
  CLUS_3                3                 52
  CLUS_4                1                 54
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    1
  16Q GAIN WILD-TYPE   19   20
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 19
  CLUS_2                1                 20
D27V4, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                0                  7
  CLUS_3                3                 18
D27V5, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                3                 86
  CLUS_2                2                 53
  CLUS_3                5                 87
D27V6, multiclass
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CLUS_1                2                 57
  CLUS_2                2                102
  CLUS_3                6                 67

Clustering(28) Variable = 17p gain mutation analysis
D28V1, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                0                 30
  CLUS_2                8                 91
  CLUS_3                0                108
D28V2, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                3                 49
  CLUS_3                1                 54
  CLUS_4                3                 52
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1    0
  17P GAIN WILD-TYPE   21   21
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                1                 21
  CLUS_2                0                 21
D28V4, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 42 
        TCGA-BR-4187         TCGA-BR-4191         TCGA-BR-4201 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-4253         TCGA-BR-4255         TCGA-BR-4256 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-4257         TCGA-BR-4267         TCGA-BR-4279 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-4280         TCGA-BR-4292         TCGA-BR-4294 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-4357         TCGA-BR-4361         TCGA-BR-4362 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-4363         TCGA-BR-4366         TCGA-BR-4367 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-4368         TCGA-BR-4369         TCGA-BR-4370 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-4371         TCGA-CG-4301         TCGA-CG-4304 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4442 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4475         TCGA-CG-4476         TCGA-CG-4477 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D28V5, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                4                 85
  CLUS_2                0                 55
  CLUS_3                4                 88
D28V6, multiclass
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  CLUS_1                2                 57
  CLUS_2                4                100
  CLUS_3                2                 71

Clustering(29) Variable = 17q gain mutation analysis
D29V1, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               11                 88
  CLUS_3                0                108
D29V2, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                3                 49
  CLUS_3                3                 52
  CLUS_4                3                 52
D29V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1    0
  17Q GAIN WILD-TYPE   21   21
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                1                 21
  CLUS_2                0                 21
D29V4, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 42 
        TCGA-BR-4187         TCGA-BR-4191         TCGA-BR-4201 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-4253         TCGA-BR-4255         TCGA-BR-4256 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-4257         TCGA-BR-4267         TCGA-BR-4279 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-4280         TCGA-BR-4292         TCGA-BR-4294 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-4357         TCGA-BR-4361         TCGA-BR-4362 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-4363         TCGA-BR-4366         TCGA-BR-4367 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-4368         TCGA-BR-4369         TCGA-BR-4370 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-4371         TCGA-CG-4301         TCGA-CG-4304 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4442 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4475         TCGA-CG-4476         TCGA-CG-4477 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
D29V5, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                7                 82
  CLUS_2                0                 55
  CLUS_3                4                 88
D29V6, multiclass
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CLUS_1                2                 57
  CLUS_2                6                 98
  CLUS_3                3                 70

Clustering(30) Variable = 18p gain mutation analysis
D30V1, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 29
  CLUS_2               12                 87
  CLUS_3                3                105
D30V2, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                2                 50
  CLUS_3                1                 54
  CLUS_4                7                 48
D30V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    3
  18P GAIN WILD-TYPE   20   18
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                3                 18
D30V4, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                1                  6
  CLUS_3                3                 18
D30V5, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                9                 80
  CLUS_2                0                 55
  CLUS_3                7                 85
D30V6, multiclass
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  CLUS_1                5                 54
  CLUS_2                8                 96
  CLUS_3                3                 70

Clustering(31) Variable = 18q gain mutation analysis
D31V1, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 29
  CLUS_2                5                 94
  CLUS_3                2                106
D31V2, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                1                 51
  CLUS_3                0                 55
  CLUS_4                3                 52
D31V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    2
  18Q GAIN WILD-TYPE   21   19
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 21
  CLUS_2                2                 19
D31V4, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                0                  7
  CLUS_3                2                 19
D31V5, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                6                 83
  CLUS_2                0                 55
  CLUS_3                2                 90
D31V6, multiclass
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CLUS_1                3                 56
  CLUS_2                5                 99
  CLUS_3                0                 73

Clustering(32) Variable = 19p gain mutation analysis
D32V1, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 29
  CLUS_2                5                 94
  CLUS_3                4                104
D32V2, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                0                 52
  CLUS_3                2                 53
  CLUS_4                2                 53
D32V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    3
  19P GAIN WILD-TYPE   21   18
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                1                 21
  CLUS_2                3                 18
D32V4, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                0                  7
  CLUS_3                1                 20
D32V5, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                7                 82
  CLUS_2                2                 53
  CLUS_3                1                 91
D32V6, multiclass
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  CLUS_1                2                 57
  CLUS_2                7                 97
  CLUS_3                1                 72

Clustering(33) Variable = 19q gain mutation analysis
D33V1, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 28
  CLUS_2               12                 87
  CLUS_3                7                101
D33V2, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                3                 24
  CLUS_2                2                 50
  CLUS_3                3                 52
  CLUS_4                7                 48
D33V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    4
  19Q GAIN WILD-TYPE   20   17
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                4                 17
D33V4, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                4                 11
  CLUS_2                0                  7
  CLUS_3                2                 19
D33V5, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                8                 81
  CLUS_2                3                 52
  CLUS_3               10                 82
D33V6, multiclass
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CLUS_1                6                 53
  CLUS_2               11                 93
  CLUS_3                4                 69

Clustering(34) Variable = 20p gain mutation analysis
D34V1, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               15                 15
  CLUS_2               59                 40
  CLUS_3               17                 91
D34V2, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               12                 15
  CLUS_2               15                 37
  CLUS_3               12                 43
  CLUS_4               29                 26
D34V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7   12
  20P GAIN WILD-TYPE   15    9
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1                7                 15
  CLUS_2               12                  9
D34V4, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               11                  4
  CLUS_2                1                  6
  CLUS_3                7                 14
D34V5, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               35                 54
  CLUS_2               15                 40
  CLUS_3               41                 51
D34V6, multiclass
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  CLUS_1               31                 28
  CLUS_2               39                 65
  CLUS_3               21                 52

Clustering(35) Variable = 20q gain mutation analysis
D35V1, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               17                 13
  CLUS_2               77                 22
  CLUS_3               21                 87
D35V2, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               14                 13
  CLUS_2               21                 31
  CLUS_3               15                 40
  CLUS_4               41                 14
D35V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8   12
  20Q GAIN WILD-TYPE   14    9
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1                8                 14
  CLUS_2               12                  9
D35V4, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               11                  4
  CLUS_2                1                  6
  CLUS_3                8                 13
D35V5, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               40                 49
  CLUS_2               18                 37
  CLUS_3               57                 35
D35V6, multiclass
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CLUS_1               39                 20
  CLUS_2               50                 54
  CLUS_3               26                 47

Clustering(36) Variable = 22q gain mutation analysis
D36V1, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                 29
  CLUS_2                3                 96
  CLUS_3                0                108
D36V2, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                0                 52
  CLUS_3                0                 55
  CLUS_4                2                 53
D36V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    0
  22Q GAIN WILD-TYPE   22   21
D36V4, multiclass
D36V5, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                 88
  CLUS_2                0                 55
  CLUS_3                3                 89
D36V6, multiclass
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CLUS_1                1                 58
  CLUS_2                3                101
  CLUS_3                0                 73

Clustering(37) Variable = 1p loss mutation analysis
D37V1, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2               9                90
  CLUS_3               0               108
D37V2, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               2                50
  CLUS_3               2                53
  CLUS_4               3                52
D37V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    0
  1P LOSS WILD-TYPE   20   21
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2                20
  CLUS_2               0                21
D37V4, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                41 
       TCGA-BR-4187        TCGA-BR-4191        TCGA-BR-4201        TCGA-BR-4253 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257        TCGA-BR-4267 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4357 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-4361        TCGA-BR-4362        TCGA-BR-4363        TCGA-BR-4366 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-4369        TCGA-BR-4370 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-4371        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4442 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4460 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4477 
"1P LOSS WILD-TYPE" 
D37V5, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               6                83
  CLUS_2               1                54
  CLUS_3               2                90
D37V6, multiclass
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  CLUS_1               2                57
  CLUS_2               4               100
  CLUS_3               3                70

Clustering(38) Variable = 2p loss mutation analysis
D38V1, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2               4                95
  CLUS_3               0               108
D38V2, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               0                52
  CLUS_3               1                54
  CLUS_4               2                53
D38V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1    0
  2P LOSS WILD-TYPE   21   21
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                21
  CLUS_2               0                21
D38V4, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                42 
       TCGA-BR-4187        TCGA-BR-4191        TCGA-BR-4201        TCGA-BR-4253 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257        TCGA-BR-4267 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362        TCGA-BR-4363 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-4369 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4370        TCGA-BR-4371        TCGA-CG-4301        TCGA-CG-4304 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4438 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4444 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4476        TCGA-CG-4477 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D38V5, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                88
  CLUS_2               1                54
  CLUS_3               2                90
D38V6, multiclass
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  CLUS_1               1                58
  CLUS_2               0               104
  CLUS_3               3                70

Clustering(39) Variable = 2q loss mutation analysis
D39V1, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2               5                94
  CLUS_3               0               108
D39V2, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               1                51
  CLUS_3               1                54
  CLUS_4               2                53
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1    0
  2Q LOSS WILD-TYPE   21   21
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                21
  CLUS_2               0                21
D39V4, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                42 
       TCGA-BR-4187        TCGA-BR-4191        TCGA-BR-4201        TCGA-BR-4253 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257        TCGA-BR-4267 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362        TCGA-BR-4363 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-4369 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BR-4370        TCGA-BR-4371        TCGA-CG-4301        TCGA-CG-4304 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4438 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4444 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CG-4476        TCGA-CG-4477 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D39V5, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               2                87
  CLUS_2               1                54
  CLUS_3               2                90
D39V6, multiclass
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CLUS_1               1                58
  CLUS_2               1               103
  CLUS_3               3                70

Clustering(40) Variable = 3p loss mutation analysis
D40V1, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2              16                83
  CLUS_3               0               108
D40V2, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               6                46
  CLUS_3               1                54
  CLUS_4               7                48
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    2
  3P LOSS WILD-TYPE   22   19
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               0                22
  CLUS_2               2                19
D40V4, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                41 
       TCGA-BR-4187        TCGA-BR-4191        TCGA-BR-4201        TCGA-BR-4253 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257        TCGA-BR-4267 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362        TCGA-BR-4363 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-4369 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-4370        TCGA-BR-4371        TCGA-CG-4301        TCGA-CG-4304 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4440 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4469 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4477 
"3P LOSS WILD-TYPE" 
D40V5, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               4                85
  CLUS_2               0                55
  CLUS_3              12                80
D40V6, multiclass
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  CLUS_1               9                50
  CLUS_2               5                99
  CLUS_3               2                71

Clustering(41) Variable = 3q loss mutation analysis
D41V1, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2               9                90
  CLUS_3               0               108
D41V2, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               2                50
  CLUS_3               0                55
  CLUS_4               5                50
D41V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    2
  3Q LOSS WILD-TYPE   22   19
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                22
  CLUS_2               2                19
D41V4, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                41 
       TCGA-BR-4187        TCGA-BR-4191        TCGA-BR-4201        TCGA-BR-4253 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257        TCGA-BR-4267 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362        TCGA-BR-4363 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-4369 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-4370        TCGA-BR-4371        TCGA-CG-4301        TCGA-CG-4304 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4440 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4469 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4477 
"3Q LOSS WILD-TYPE" 
D41V5, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               0                89
  CLUS_2               0                55
  CLUS_3               9                83
D41V6, multiclass
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CLUS_1               6                53
  CLUS_2               1               103
  CLUS_3               2                71

Clustering(42) Variable = 4p loss mutation analysis
D42V1, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2              34                65
  CLUS_3               4               104
D42V2, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               6                46
  CLUS_3               8                47
  CLUS_4              15                40
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3    5
  4P LOSS WILD-TYPE   19   16
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               3                19
  CLUS_2               5                16
D42V4, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1               4                11
  CLUS_2               1                 6
  CLUS_3               3                18
D42V5, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              12                77
  CLUS_2               3                52
  CLUS_3              22                70
D42V6, multiclass
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  CLUS_1              23                36
  CLUS_2               9                95
  CLUS_3               5                68

Clustering(43) Variable = 4q loss mutation analysis
D43V1, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2              32                67
  CLUS_3               2               106
D43V2, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               7                45
  CLUS_3               6                49
  CLUS_4              15                40
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2    4
  4Q LOSS WILD-TYPE   20   17
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               2                20
  CLUS_2               4                17
D43V4, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1               3                12
  CLUS_2               1                 6
  CLUS_3               2                19
D43V5, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              11                78
  CLUS_2               2                53
  CLUS_3              20                72
D43V6, multiclass
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CLUS_1              21                38
  CLUS_2               8                96
  CLUS_3               4                69

Clustering(44) Variable = 5p loss mutation analysis
D44V1, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2              13                86
  CLUS_3               0               108
D44V2, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               4                48
  CLUS_3               1                54
  CLUS_4               6                49
D44V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    0
  5P LOSS WILD-TYPE   20   21
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               2                20
  CLUS_2               0                21
D44V4, multiclass
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                41 
       TCGA-BR-4187        TCGA-BR-4191        TCGA-BR-4201        TCGA-BR-4253 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257        TCGA-BR-4267 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362        TCGA-BR-4363 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-4366        TCGA-BR-4368        TCGA-BR-4369        TCGA-BR-4370 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-4371        TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4438        TCGA-CG-4440 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4460 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4477 
"5P LOSS WILD-TYPE" 
D44V5, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               3                86
  CLUS_2               2                53
  CLUS_3               7                85
D44V6, multiclass
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  CLUS_1               6                53
  CLUS_2               4               100
  CLUS_3               2                71

Clustering(45) Variable = 5q loss mutation analysis
D45V1, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2              25                74
  CLUS_3               0               108
D45V2, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               6                46
  CLUS_3               3                52
  CLUS_4              13                42
D45V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2    1
  5Q LOSS WILD-TYPE   20   20
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               2                20
  CLUS_2               1                20
D45V4, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               1                14
  CLUS_2               0                 7
  CLUS_3               2                19
D45V5, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1               6                83
  CLUS_2               2                53
  CLUS_3              16                76
D45V6, multiclass
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CLUS_1              15                44
  CLUS_2               7                97
  CLUS_3               2                71

Clustering(46) Variable = 6p loss mutation analysis
D46V1, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2               8                91
  CLUS_3               2               106
D46V2, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               1                51
  CLUS_3               3                52
  CLUS_4               4                51
D46V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2    0
  6P LOSS WILD-TYPE   20   21
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               2                20
  CLUS_2               0                21
D46V4, multiclass
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2                41 
       TCGA-BR-4187        TCGA-BR-4191        TCGA-BR-4201        TCGA-BR-4253 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257        TCGA-BR-4267 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4357 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-4361        TCGA-BR-4362        TCGA-BR-4366        TCGA-BR-4367 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-4368        TCGA-BR-4369        TCGA-BR-4370        TCGA-BR-4371 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4442 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4460 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4477 
"6P LOSS WILD-TYPE" 
D46V5, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               6                83
  CLUS_2               3                52
  CLUS_3               1                91
D46V6, multiclass
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  CLUS_1               4                55
  CLUS_2               3               101
  CLUS_3               3                70

Clustering(47) Variable = 6q loss mutation analysis
D47V1, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2              13                86
  CLUS_3               3               105
D47V2, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               1                51
  CLUS_3               4                51
  CLUS_4               7                48
D47V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3    1
  6Q LOSS WILD-TYPE   19   20
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               3                19
  CLUS_2               1                20
D47V4, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               0                15
  CLUS_2               3                 4
  CLUS_3               1                20
D47V5, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               9                80
  CLUS_2               3                52
  CLUS_3               4                88
D47V6, multiclass
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CLUS_1               6                53
  CLUS_2               6                98
  CLUS_3               4                69

Clustering(48) Variable = 7p loss mutation analysis
D48V1, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2               4                95
  CLUS_3               0               108
D48V2, multiclass
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2               187 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6453 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707        TCGA-BR-7715 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7851 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7958        TCGA-BR-7959 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8058        TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        TCGA-BR-8360 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8361        TCGA-BR-8362        TCGA-BR-8363        TCGA-BR-8364 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8365        TCGA-BR-8366        TCGA-BR-8367        TCGA-BR-8368 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8369        TCGA-BR-8370        TCGA-BR-8371        TCGA-BR-8372 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8373        TCGA-BR-8380        TCGA-BR-8381        TCGA-BR-8382 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8384        TCGA-BR-8483        TCGA-BR-8484        TCGA-BR-8485 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8486        TCGA-BR-8487        TCGA-BR-8588        TCGA-BR-8589 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8590        TCGA-BR-8591        TCGA-BR-8592        TCGA-BR-8676 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8677        TCGA-BR-8678        TCGA-BR-8679        TCGA-BR-8680 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8682        TCGA-BR-8683        TCGA-BR-8686        TCGA-BR-8687 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8690        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-8524        TCGA-CD-8525        TCGA-CD-8526        TCGA-CD-8527 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-8528        TCGA-CD-8529        TCGA-CD-8530        TCGA-CD-8531 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-8532        TCGA-CD-8533        TCGA-CD-8534        TCGA-CD-8535 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-8536        TCGA-CG-4437        TCGA-CG-4441        TCGA-CG-5716 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-D7-8570        TCGA-D7-8572 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-8573        TCGA-D7-8574        TCGA-D7-8575        TCGA-D7-8576 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-8578        TCGA-D7-8579        TCGA-EQ-5647        TCGA-EQ-8122 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8211        TCGA-FP-8631 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HF-7131        TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HF-7136        TCGA-HJ-7597        TCGA-HU-8238        TCGA-HU-8243 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HU-8245        TCGA-HU-8249        TCGA-HU-8602        TCGA-HU-8604 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HU-8608        TCGA-HU-8610        TCGA-IN-7806        TCGA-IN-7808 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IN-8462        TCGA-IN-8663        TCGA-IP-7968 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
D48V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    2
  7P LOSS WILD-TYPE   22   19
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               0                22
  CLUS_2               2                19
D48V4, multiclass
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2                41 
       TCGA-BR-4187        TCGA-BR-4191        TCGA-BR-4201        TCGA-BR-4253 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257        TCGA-BR-4267 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362        TCGA-BR-4363 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-4369 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-4370        TCGA-BR-4371        TCGA-CG-4301        TCGA-CG-4304 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4440 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4442        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4460 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4477 
"7P LOSS WILD-TYPE" 
D48V5, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               1                88
  CLUS_2               0                55
  CLUS_3               3                89
D48V6, multiclass
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  CLUS_1               2                57
  CLUS_2               2               102
  CLUS_3               0                73

Clustering(49) Variable = 7q loss mutation analysis
D49V1, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2               9                90
  CLUS_3               0               108
D49V2, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               2                50
  CLUS_3               0                55
  CLUS_4               5                50
D49V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    2
  7Q LOSS WILD-TYPE   22   19
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               0                22
  CLUS_2               2                19
D49V4, multiclass
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2                41 
       TCGA-BR-4187        TCGA-BR-4191        TCGA-BR-4201        TCGA-BR-4253 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257        TCGA-BR-4267 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362        TCGA-BR-4363 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-4369 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-4370        TCGA-BR-4371        TCGA-CG-4301        TCGA-CG-4304 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4440 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4442        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4460 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4477 
"7Q LOSS WILD-TYPE" 
D49V5, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               1                88
  CLUS_2               0                55
  CLUS_3               8                84
D49V6, multiclass
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CLUS_1               5                54
  CLUS_2               4               100
  CLUS_3               0                73

Clustering(50) Variable = 8p loss mutation analysis
D50V1, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2              16                83
  CLUS_3               1               107
D50V2, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               3                49
  CLUS_3               3                52
  CLUS_4               5                50
D50V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    2
  8P LOSS WILD-TYPE   18   19
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               4                18
  CLUS_2               2                19
D50V4, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               1                14
  CLUS_2               1                 6
  CLUS_3               4                17
D50V5, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               6                83
  CLUS_2               0                55
  CLUS_3              10                82
D50V6, multiclass
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  CLUS_1               9                50
  CLUS_2               5                99
  CLUS_3               2                71

Clustering(51) Variable = 8q loss mutation analysis
D51V1, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2               5                94
  CLUS_3               0               108
D51V2, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               0                27
  CLUS_2               1                51
  CLUS_3               0                55
  CLUS_4               2                53
D51V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    1
  8Q LOSS WILD-TYPE   21   20
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               1                21
  CLUS_2               1                20
D51V4, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                41 
       TCGA-BR-4187        TCGA-BR-4201        TCGA-BR-4253        TCGA-BR-4255 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4256        TCGA-BR-4257        TCGA-BR-4267        TCGA-BR-4279 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4357        TCGA-BR-4361 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4362        TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4367 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4368        TCGA-BR-4369        TCGA-BR-4370        TCGA-BR-4371 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4442 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4460 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4477 
"8Q LOSS WILD-TYPE" 
D51V5, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               3                86
  CLUS_2               0                55
  CLUS_3               2                90
D51V6, multiclass
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CLUS_1               4                55
  CLUS_2               1               103
  CLUS_3               0                73

Clustering(52) Variable = 9p loss mutation analysis
D52V1, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                29
  CLUS_2              36                63
  CLUS_3               1               107
D52V2, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               5                47
  CLUS_3               5                50
  CLUS_4              19                36
D52V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4    4
  9P LOSS WILD-TYPE   18   17
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               4                18
  CLUS_2               4                17
D52V4, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1               3                12
  CLUS_2               1                 6
  CLUS_3               4                17
D52V5, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              12                77
  CLUS_2               3                52
  CLUS_3              22                70
D52V6, multiclass
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  CLUS_1              17                42
  CLUS_2              14                90
  CLUS_3               6                67

Clustering(53) Variable = 9q loss mutation analysis
D53V1, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                29
  CLUS_2              18                81
  CLUS_3               1               107
D53V2, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               3                49
  CLUS_3               1                54
  CLUS_4              13                42
D53V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2    0
  9Q LOSS WILD-TYPE   20   21
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               2                20
  CLUS_2               0                21
D53V4, multiclass
[1] "Remove cluster labels:" "9Q LOSS MUTATED"       
clus
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                41 
       TCGA-BR-4187        TCGA-BR-4191        TCGA-BR-4201        TCGA-BR-4253 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257        TCGA-BR-4267 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362        TCGA-BR-4363 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-4366        TCGA-BR-4368        TCGA-BR-4369        TCGA-BR-4370 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-4371        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4442 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4460 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4477 
"9Q LOSS WILD-TYPE" 
D53V5, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               6                83
  CLUS_2               2                53
  CLUS_3              12                80
D53V6, multiclass
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CLUS_1               9                50
  CLUS_2               9                95
  CLUS_3               2                71

Clustering(54) Variable = 10p loss mutation analysis
D54V1, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               14                 85
  CLUS_3                0                108
D54V2, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                3                 49
  CLUS_3                0                 55
  CLUS_4                7                 48
D54V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2    2
  10P LOSS WILD-TYPE   20   19
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                2                 19
D54V4, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                2                  5
  CLUS_3                1                 20
D54V5, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                 83
  CLUS_2                1                 54
  CLUS_3                7                 85
D54V6, multiclass
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  CLUS_1                6                 53
  CLUS_2                5                 99
  CLUS_3                3                 70

Clustering(55) Variable = 10q loss mutation analysis
D55V1, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               14                 85
  CLUS_3                0                108
D55V2, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                3                 49
  CLUS_3                0                 55
  CLUS_4                7                 48
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1    3
  10Q LOSS WILD-TYPE   21   18
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                1                 21
  CLUS_2                3                 18
D55V4, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                1                  6
  CLUS_3                1                 20
D55V5, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                5                 84
  CLUS_2                1                 54
  CLUS_3                8                 84
D55V6, multiclass
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CLUS_1                6                 53
  CLUS_2                6                 98
  CLUS_3                2                 71

Clustering(56) Variable = 11p loss mutation analysis
D56V1, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               13                 86
  CLUS_3                2                106
D56V2, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                1                 51
  CLUS_3                2                 53
  CLUS_4                7                 48
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3    2
  11P LOSS WILD-TYPE   19   19
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                3                 19
  CLUS_2                2                 19
D56V4, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                0                 15
  CLUS_2                2                  5
  CLUS_3                3                 18
D56V5, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1               10                 79
  CLUS_2                1                 54
  CLUS_3                4                 88
D56V6, multiclass
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  CLUS_1                7                 52
  CLUS_2                6                 98
  CLUS_3                2                 71

Clustering(57) Variable = 11q loss mutation analysis
D57V1, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               10                 89
  CLUS_3                1                107
D57V2, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                2                 50
  CLUS_3                1                 54
  CLUS_4                5                 50
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2    1
  11Q LOSS WILD-TYPE   20   20
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                1                 20
D57V4, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                0                 15
  CLUS_2                1                  6
  CLUS_3                2                 19
D57V5, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                8                 81
  CLUS_2                1                 54
  CLUS_3                2                 90
D57V6, multiclass
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CLUS_1                5                 54
  CLUS_2                4                100
  CLUS_3                2                 71

Clustering(58) Variable = 12p loss mutation analysis
D58V1, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               14                 85
  CLUS_3                1                107
D58V2, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                2                 50
  CLUS_3                3                 52
  CLUS_4                7                 48
D58V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0    3
  12P LOSS WILD-TYPE   22   18
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                0                 22
  CLUS_2                3                 18
D58V4, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                2                  5
  CLUS_3                0                 21
D58V5, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                5                 84
  CLUS_2                1                 54
  CLUS_3                9                 83
D58V6, multiclass
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  CLUS_1                7                 52
  CLUS_2                6                 98
  CLUS_3                2                 71

Clustering(59) Variable = 12q loss mutation analysis
D59V1, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2                8                 91
  CLUS_3                0                108
D59V2, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                0                 52
  CLUS_3                1                 54
  CLUS_4                5                 50
D59V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    2
  12Q LOSS WILD-TYPE   22   19
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                0                 22
  CLUS_2                2                 19
D59V4, multiclass
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                 41 
        TCGA-BR-4187         TCGA-BR-4191         TCGA-BR-4201 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-4253         TCGA-BR-4255         TCGA-BR-4256 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-4257         TCGA-BR-4267         TCGA-BR-4279 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-4280         TCGA-BR-4292         TCGA-BR-4294 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-4357         TCGA-BR-4361         TCGA-BR-4362 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-4363         TCGA-BR-4366         TCGA-BR-4367 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-4368         TCGA-BR-4369         TCGA-BR-4370 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-4371         TCGA-CG-4301         TCGA-CG-4304 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4438 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4442         TCGA-CG-4444 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4460         TCGA-CG-4462 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4475 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4476         TCGA-CG-4477 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
D59V5, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                4                 85
  CLUS_2                0                 55
  CLUS_3                4                 88
D59V6, multiclass
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CLUS_1                5                 54
  CLUS_2                2                102
  CLUS_3                1                 72

Clustering(60) Variable = 13q loss mutation analysis
D60V1, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2                8                 91
  CLUS_3                0                108
D60V2, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                2                 50
  CLUS_3                0                 55
  CLUS_4                3                 52
D60V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3    0
  13Q LOSS WILD-TYPE   19   21
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                3                 19
  CLUS_2                0                 21
D60V4, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                0                 15
  CLUS_2                0                  7
  CLUS_3                3                 18
D60V5, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                4                 85
  CLUS_2                0                 55
  CLUS_3                4                 88
D60V6, multiclass
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CLUS_1                3                 56
  CLUS_2                3                101
  CLUS_3                2                 71

Clustering(61) Variable = 14q loss mutation analysis
D61V1, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                1                 29
  CLUS_2               16                 83
  CLUS_3                2                106
D61V2, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                3                 49
  CLUS_3                2                 53
  CLUS_4                9                 46
D61V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1    3
  14Q LOSS WILD-TYPE   21   18
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                1                 21
  CLUS_2                3                 18
D61V4, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                1                  6
  CLUS_3                1                 20
D61V5, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                3                 86
  CLUS_2                4                 51
  CLUS_3               12                 80
D61V6, multiclass
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CLUS_1                9                 50
  CLUS_2                5                 99
  CLUS_3                5                 68

Clustering(62) Variable = 15q loss mutation analysis
D62V1, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               15                 84
  CLUS_3                0                108
D62V2, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                3                 49
  CLUS_3                1                 54
  CLUS_4                8                 47
D62V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    2
  15Q LOSS WILD-TYPE   21   19
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                1                 21
  CLUS_2                2                 19
D62V4, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                0                  7
  CLUS_3                1                 20
D62V5, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                5                 84
  CLUS_2                2                 53
  CLUS_3                8                 84
D62V6, multiclass
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CLUS_1                6                 53
  CLUS_2                7                 97
  CLUS_3                2                 71

Clustering(63) Variable = 16p loss mutation analysis
D63V1, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               11                 88
  CLUS_3                0                108
D63V2, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                3                 49
  CLUS_3                1                 54
  CLUS_4                3                 52
D63V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2    2
  16P LOSS WILD-TYPE   20   19
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                2                 19
D63V4, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                1                  6
  CLUS_3                2                 19
D63V5, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                4                 85
  CLUS_2                0                 55
  CLUS_3                6                 86
D63V6, multiclass
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  CLUS_1                5                 54
  CLUS_2                4                100
  CLUS_3                1                 72

Clustering(64) Variable = 16q loss mutation analysis
D64V1, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               16                 83
  CLUS_3                1                107
D64V2, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                2                 50
  CLUS_3                2                 53
  CLUS_4                7                 48
D64V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    3
  16Q LOSS WILD-TYPE   19   18
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                3                 19
  CLUS_2                3                 18
D64V4, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                1                 14
  CLUS_2                2                  5
  CLUS_3                3                 18
D64V5, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                8                 81
  CLUS_2                0                 55
  CLUS_3                8                 84
D64V6, multiclass
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CLUS_1                7                 52
  CLUS_2                6                 98
  CLUS_3                3                 70

Clustering(65) Variable = 17p loss mutation analysis
D65V1, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                1                 29
  CLUS_2               42                 57
  CLUS_3                3                105
D65V2, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                7                 45
  CLUS_3                5                 50
  CLUS_4               22                 33
D65V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3    6
  17P LOSS WILD-TYPE   19   15
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                3                 19
  CLUS_2                6                 15
D65V4, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1                4                 11
  CLUS_2                3                  4
  CLUS_3                2                 19
D65V5, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               17                 72
  CLUS_2                3                 52
  CLUS_3               26                 66
D65V6, multiclass
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  CLUS_1               22                 37
  CLUS_2               17                 87
  CLUS_3                7                 66

Clustering(66) Variable = 17q loss mutation analysis
D66V1, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 29
  CLUS_2               13                 86
  CLUS_3                1                107
D66V2, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                2                 50
  CLUS_3                2                 53
  CLUS_4                4                 51
D66V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    3
  17Q LOSS WILD-TYPE   20   18
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                3                 18
D66V4, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                1                  6
  CLUS_3                2                 19
D66V5, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                4                 85
  CLUS_2                1                 54
  CLUS_3               10                 82
D66V6, multiclass
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CLUS_1                8                 51
  CLUS_2                6                 98
  CLUS_3                1                 72

Clustering(67) Variable = 18p loss mutation analysis
D67V1, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               18                 81
  CLUS_3                6                102
D67V2, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 24
  CLUS_2                1                 51
  CLUS_3                4                 51
  CLUS_4                9                 46
D67V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3    4
  18P LOSS WILD-TYPE   19   17
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 19
  CLUS_2                4                 17
D67V4, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                3                 12
  CLUS_2                1                  6
  CLUS_3                3                 18
D67V5, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1                7                 82
  CLUS_2                3                 52
  CLUS_3               13                 79
D67V6, multiclass
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  CLUS_1               10                 49
  CLUS_2                8                 96
  CLUS_3                5                 68

Clustering(68) Variable = 18q loss mutation analysis
D68V1, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               30                 69
  CLUS_3                7                101
D68V2, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                5                 22
  CLUS_2                4                 48
  CLUS_3                5                 50
  CLUS_4               11                 44
D68V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      7    5
  18Q LOSS WILD-TYPE   15   16
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                7                 15
  CLUS_2                5                 16
D68V4, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1                4                 11
  CLUS_2                2                  5
  CLUS_3                6                 15
D68V5, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               17                 72
  CLUS_2                4                 51
  CLUS_3               15                 77
D68V6, multiclass
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CLUS_1               12                 47
  CLUS_2               17                 87
  CLUS_3                7                 66

Clustering(69) Variable = 19p loss mutation analysis
D69V1, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               23                 76
  CLUS_3                0                108
D69V2, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                5                 47
  CLUS_3                3                 52
  CLUS_4                9                 46
D69V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    6
  19P LOSS WILD-TYPE   22   15
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                0                 22
  CLUS_2                6                 15
D69V4, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                5                 10
  CLUS_2                1                  6
  CLUS_3                0                 21
D69V5, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1                7                 82
  CLUS_2                3                 52
  CLUS_3               13                 79
D69V6, multiclass
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  CLUS_1               13                 46
  CLUS_2                7                 97
  CLUS_3                3                 70

Clustering(70) Variable = 19q loss mutation analysis
D70V1, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               16                 83
  CLUS_3                0                108
D70V2, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                2                 50
  CLUS_3                1                 54
  CLUS_4                8                 47
D70V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0    5
  19Q LOSS WILD-TYPE   22   16
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                0                 22
  CLUS_2                5                 16
D70V4, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                4                 11
  CLUS_2                1                  6
  CLUS_3                0                 21
D70V5, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1                5                 84
  CLUS_2                1                 54
  CLUS_3               10                 82
D70V6, multiclass
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CLUS_1               10                 49
  CLUS_2                4                100
  CLUS_3                2                 71

Clustering(71) Variable = 20p loss mutation analysis
D71V1, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                 29
  CLUS_2                6                 93
  CLUS_3                0                108
D71V2, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                1                 26
  CLUS_2                0                 52
  CLUS_3                0                 55
  CLUS_4                4                 51
D71V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2    0
  20P LOSS WILD-TYPE   20   21
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                 20
  CLUS_2                0                 21
D71V4, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 41 
        TCGA-BR-4187         TCGA-BR-4191         TCGA-BR-4201 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-4253         TCGA-BR-4255         TCGA-BR-4256 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-4257         TCGA-BR-4279         TCGA-BR-4280 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-4292         TCGA-BR-4294         TCGA-BR-4357 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-4361         TCGA-BR-4362         TCGA-BR-4363 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-4366         TCGA-BR-4367         TCGA-BR-4368 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-4369         TCGA-BR-4370         TCGA-BR-4371 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4438         TCGA-CG-4440 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4442         TCGA-CG-4443         TCGA-CG-4444 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4460         TCGA-CG-4462 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4475 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4476         TCGA-CG-4477 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D71V5, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                4                 85
  CLUS_2                0                 55
  CLUS_3                3                 89
D71V6, multiclass
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  CLUS_1                2                 57
  CLUS_2                4                100
  CLUS_3                1                 72

Clustering(72) Variable = 21q loss mutation analysis
D72V1, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 27
  CLUS_2               35                 64
  CLUS_3                4                104
D72V2, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                2                 25
  CLUS_2                9                 43
  CLUS_3                5                 50
  CLUS_4               16                 39
D72V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    6
  21Q LOSS WILD-TYPE   19   15
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                3                 19
  CLUS_2                6                 15
D72V4, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1                4                 11
  CLUS_2                3                  4
  CLUS_3                2                 19
D72V5, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               15                 74
  CLUS_2                3                 52
  CLUS_3               24                 68
D72V6, multiclass
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CLUS_1               13                 46
  CLUS_2               19                 85
  CLUS_3               10                 63

Clustering(73) Variable = 22q loss mutation analysis
D73V1, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                 30
  CLUS_2               30                 69
  CLUS_3                0                108
D73V2, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                0                 27
  CLUS_2                6                 46
  CLUS_3                2                 53
  CLUS_4               15                 40
D73V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4    2
  22Q LOSS WILD-TYPE   18   19
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                4                 18
  CLUS_2                2                 19
D73V4, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1                2                 13
  CLUS_2                1                  6
  CLUS_3                3                 18
D73V5, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               11                 78
  CLUS_2                0                 55
  CLUS_3               19                 73
D73V6, multiclass
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CLUS_1               16                 43
  CLUS_2               10                 94
  CLUS_3                4                 69

Clustering(74) Variable = Xq loss mutation analysis
D74V1, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               0                30
  CLUS_2               9                90
  CLUS_3               3               105
D74V2, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                26
  CLUS_2               4                48
  CLUS_3               1                54
  CLUS_4               3                52
D74V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    2
  XQ LOSS WILD-TYPE   21   19
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                21
  CLUS_2               2                19
D74V4, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               1                14
  CLUS_2               1                 6
  CLUS_3               1                20
D74V5, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               4                85
  CLUS_2               1                54
  CLUS_3               7                85
D74V6, multiclass
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CLUS_1               2                57
  CLUS_2               8                96
  CLUS_3               2                71
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"          "MRNASEQ_CNMF" 
                     V4                      V5                      V6 
"MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
