
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/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Cluster_cnvarms_onlysig/broadinstitute.org/cancer.genome.analysis/00508/6/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Cluster_cnvarms_onlysig/broadinstitute.org/cancer.genome.analysis/00508/6/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/BLCA-TP/3472512/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/BLCA-TP/3537480/BLCA-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=BLCA-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=BLCA-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=153, in cluster file=150, common to both=150
[1] "Reduce the number of clustering variables from 80 to 76."
[1]  76 150
[1] "1p gain"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
               17               133 
      1P GAIN CNV 1P GAIN WILD-TYPE 
               17               133 
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               33               117 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               33               117 
[1] "2p gain"
[1] 3
      2P GAIN CNV 2P GAIN WILD-TYPE 
               30               120 
      2P GAIN CNV 2P GAIN WILD-TYPE 
               30               120 
[1] "2q gain"
[1] 3
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               11               139 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               11               139 
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
               28               122 
      3P GAIN CNV 3P GAIN WILD-TYPE 
               28               122 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               42               108 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               42               108 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
                8               142 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                8               142 
[1] "4q gain"
[1] 3
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                3               147 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                3               147 
[1] "5p gain"
[1] 3
      5P GAIN CNV 5P GAIN WILD-TYPE 
               41               109 
      5P GAIN CNV 5P GAIN WILD-TYPE 
               41               109 
[1] "5q gain"
[1] 3
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               17               133 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               17               133 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
               11               139 
      6P GAIN CNV 6P GAIN WILD-TYPE 
               11               139 
[1] "6q gain"
[1] 3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                6               144 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                6               144 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
               45               105 
      7P GAIN CNV 7P GAIN WILD-TYPE 
               45               105 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               41               109 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               41               109 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
               15               135 
      8P GAIN CNV 8P GAIN WILD-TYPE 
               15               135 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               44               106 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               44               106 
[1] "9p gain"
[1] 3
      9P GAIN CNV 9P GAIN WILD-TYPE 
               15               135 
      9P GAIN CNV 9P GAIN WILD-TYPE 
               15               135 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
               12               138 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
               12               138 
[1] "10p gain"
[1] 3
      10P GAIN CNV 10P GAIN WILD-TYPE 
                27                123 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                27                123 
[1] "10q gain"
[1] 3
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 7                143 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 7                143 
[1] "11p gain"
[1] 3
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 7                143 
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 7                143 
[1] "11q gain"
[1] 3
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 9                141 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 9                141 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                26                124 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                26                124 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                18                132 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                18                132 
[1] "13q gain"
[1] 3
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                24                126 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                24                126 
[1] "14q gain"
[1] 3
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                11                139 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                11                139 
[1] "15q gain"
[1] 3
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 5                145 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 5                145 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 9                141 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 9                141 
[1] "16q gain"
[1] 3
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                13                137 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                13                137 
[1] "17p gain"
[1] 3
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 8                142 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 8                142 
[1] "17q gain"
[1] 3
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                24                126 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                24                126 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                24                126 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                24                126 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 9                141 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 9                141 
[1] "19p gain"
[1] 3
      19P GAIN CNV 19P GAIN WILD-TYPE 
                13                137 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                13                137 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                27                123 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                27                123 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                54                 96 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                54                 96 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                60                 90 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                60                 90 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                27                123 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                27                123 
[1] "22q gain"
[1] 3
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                12                138 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                12                138 
[1] "Xq gain"
[1] 3
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                6               144 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                6               144 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
                4               146 
      1P LOSS CNV 1P LOSS WILD-TYPE 
                4               146 
[1] "2p loss"
[1] 3
      2P LOSS CNV 2P LOSS WILD-TYPE 
                8               142 
      2P LOSS CNV 2P LOSS WILD-TYPE 
                8               142 
[1] "2q loss"
[1] 3
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
               17               133 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
               17               133 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
                9               141 
      3P LOSS CNV 3P LOSS WILD-TYPE 
                9               141 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
               29               121 
      4P LOSS CNV 4P LOSS WILD-TYPE 
               29               121 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               27               123 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               27               123 
[1] "5p loss"
[1] 3
      5P LOSS CNV 5P LOSS WILD-TYPE 
               14               136 
      5P LOSS CNV 5P LOSS WILD-TYPE 
               14               136 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               35               115 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               35               115 
[1] "6p loss"
[1] 3
      6P LOSS CNV 6P LOSS WILD-TYPE 
               20               130 
      6P LOSS CNV 6P LOSS WILD-TYPE 
               20               130 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               29               121 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               29               121 
[1] "7q loss"
[1] 3
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                3               147 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                3               147 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
               48               102 
      8P LOSS CNV 8P LOSS WILD-TYPE 
               48               102 
[1] "8q loss"
[1] 3
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                6               144 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                6               144 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
               43               107 
      9P LOSS CNV 9P LOSS WILD-TYPE 
               43               107 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               41               109 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               41               109 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                19                131 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                19                131 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                30                120 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                30                120 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                47                103 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                47                103 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                34                116 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                34                116 
[1] "12p loss"
[1] 3
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 6                144 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 6                144 
[1] "12q loss"
[1] 3
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 7                143 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 7                143 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                20                130 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                20                130 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                25                125 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                25                125 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                19                131 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                19                131 
[1] "16p loss"
[1] 3
      16P LOSS CNV 16P LOSS WILD-TYPE 
                17                133 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                17                133 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                17                133 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                17                133 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
                43                107 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                43                107 
[1] "17q loss"
[1] 3
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 6                144 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 6                144 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                21                129 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                21                129 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                37                113 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                37                113 
[1] "19p loss"
[1] 3
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 9                141 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 9                141 
[1] "19q loss"
[1] 3
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 4                146 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 4                146 
[1] "20p loss"
[1] 3
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 7                143 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 7                143 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                16                134 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                16                134 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                29                121 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                29                121 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                3               147 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                3               147 
[1] "data2feature, selection="
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 10 rows and 150 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:'RPPA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "CN_CNMF"                     "METHLYATION_CNMF"           
 [3] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [5] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [7] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
 [9] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 150 columns, 0 survival variables, and 10 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=5, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain
D1V1, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          10                35
  CLUS_2           0                69
  CLUS_3           7                29
D1V2, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           8                29
  CLUS_2           6                43
  CLUS_3           2                38
  CLUS_4           1                23
D1V3, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           2                 9
  CLUS_2           0                10
  CLUS_3           1                13
  CLUS_4           3                13
D1V4, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           2                11
  CLUS_2           2                12
  CLUS_3           2                22
D1V5, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           3                52
  CLUS_2           7                16
  CLUS_3           5                40
  CLUS_4           2                23
D1V6, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           3                27
  CLUS_2           4                51
  CLUS_3          10                53
D1V7, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           3                31
  CLUS_2          11                57
  CLUS_3           3                45
D1V8, multiclass
D1V9, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           2                28
  CLUS_2           4                45
  CLUS_3          11                60
D1V10, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           2                23
  CLUS_2           3                33
  CLUS_3          12                77

Clustering(2) Variable = 1q gain
D2V1, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          16                29
  CLUS_2           9                60
  CLUS_3           8                28
D2V2, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          11                26
  CLUS_2           8                41
  CLUS_3          11                29
  CLUS_4           3                21
D2V3, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           2                 9
  CLUS_2           3                 7
  CLUS_3           3                11
  CLUS_4           4                12
D2V4, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           3                10
  CLUS_2           2                12
  CLUS_3           7                17
D2V5, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          11                44
  CLUS_2          10                13
  CLUS_3           8                37
  CLUS_4           4                21
D2V6, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           9                21
  CLUS_2          11                44
  CLUS_3          13                50
D2V7, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           5                29
  CLUS_2          17                51
  CLUS_3          11                37
D2V8, multiclass
D2V9, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           4                26
  CLUS_2          10                39
  CLUS_3          19                52
D2V10, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           3                22
  CLUS_2           8                28
  CLUS_3          22                67

Clustering(3) Variable = 2p gain
D3V1, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          18                27
  CLUS_2           4                65
  CLUS_3           8                28
D3V2, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          18                19
  CLUS_2           6                43
  CLUS_3           5                35
  CLUS_4           1                23
D3V3, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           1                10
  CLUS_2           1                 9
  CLUS_3           6                 8
  CLUS_4           4                12
D3V4, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           3                10
  CLUS_2           2                12
  CLUS_3           7                17
D3V5, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          13                42
  CLUS_2           9                14
  CLUS_3           5                40
  CLUS_4           3                22
D3V6, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           4                26
  CLUS_2          14                41
  CLUS_3          12                51
D3V7, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          11                23
  CLUS_2          13                55
  CLUS_3           6                42
D3V8, multiclass
D3V9, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           9                21
  CLUS_2           7                42
  CLUS_3          14                57
D3V10, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          10                15
  CLUS_2           4                32
  CLUS_3          16                73

Clustering(4) Variable = 2q gain
D4V1, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           7                38
  CLUS_2           1                68
  CLUS_3           3                33
D4V2, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           6                31
  CLUS_2           2                47
  CLUS_3           3                37
  CLUS_4           0                24
D4V3, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           0                11
  CLUS_2           0                10
  CLUS_3           1                13
  CLUS_4           2                14
D4V4, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           1                12
  CLUS_2           0                14
  CLUS_3           2                22
D4V5, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           5                50
  CLUS_2           5                18
  CLUS_3           1                44
  CLUS_4           0                25
D4V6, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           1                29
  CLUS_2           7                48
  CLUS_3           3                60
D4V7, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           5                29
  CLUS_2           3                65
  CLUS_3           3                45
D4V8, multiclass
D4V9, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           4                26
  CLUS_2           3                46
  CLUS_3           4                67
D4V10, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           5                20
  CLUS_2           1                35
  CLUS_3           5                84

Clustering(5) Variable = 3p gain
D5V1, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1          18                27
  CLUS_2           6                63
  CLUS_3           4                32
D5V2, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           8                29
  CLUS_2           3                46
  CLUS_3          11                29
  CLUS_4           6                18
D5V3, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0                11
  CLUS_2           4                 6
  CLUS_3           4                10
  CLUS_4           1                15
D5V4, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           1                12
  CLUS_2           0                14
  CLUS_3           8                16
D5V5, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1          15                40
  CLUS_2           5                18
  CLUS_3           3                42
  CLUS_4           5                20
D5V6, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1          10                20
  CLUS_2          14                41
  CLUS_3           4                59
D5V7, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1          12                22
  CLUS_2           7                61
  CLUS_3           9                39
D5V8, multiclass
D5V9, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1          11                19
  CLUS_2           9                40
  CLUS_3           8                63
D5V10, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           8                17
  CLUS_2           9                27
  CLUS_3          11                78

Clustering(6) Variable = 3q gain
D6V1, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          25                20
  CLUS_2           9                60
  CLUS_3           8                28
D6V2, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          14                23
  CLUS_2           8                41
  CLUS_3          13                27
  CLUS_4           7                17
D6V3, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           3                 8
  CLUS_2           3                 7
  CLUS_3           4                10
  CLUS_4           4                12
D6V4, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           2                11
  CLUS_2           2                12
  CLUS_3          10                14
D6V5, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          17                38
  CLUS_2          10                13
  CLUS_3          10                35
  CLUS_4           5                20
D6V6, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           9                21
  CLUS_2          20                35
  CLUS_3          13                50
D6V7, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          14                20
  CLUS_2          17                51
  CLUS_3          11                37
D6V8, multiclass
D6V9, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          13                17
  CLUS_2          11                38
  CLUS_3          18                53
D6V10, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          11                14
  CLUS_2           9                27
  CLUS_3          22                67

Clustering(7) Variable = 4p gain
D7V1, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           3                42
  CLUS_2           3                66
  CLUS_3           2                34
D7V2, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           3                34
  CLUS_2           3                46
  CLUS_3           2                38
  CLUS_4           0                24
D7V3, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           1                10
  CLUS_2           1                 9
  CLUS_3           2                12
  CLUS_4           2                14
D7V4, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           1                12
  CLUS_2           2                12
  CLUS_3           3                21
D7V5, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           3                52
  CLUS_2           1                22
  CLUS_3           3                42
  CLUS_4           1                24
D7V6, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           1                29
  CLUS_2           3                52
  CLUS_3           4                59
D7V7, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           2                32
  CLUS_2           5                63
  CLUS_3           1                47
D7V8, multiclass
D7V9, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           2                28
  CLUS_2           1                48
  CLUS_3           5                66
D7V10, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           1                24
  CLUS_2           2                34
  CLUS_3           5                84

Clustering(8) Variable = 4q gain
D8V1, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           1                44
  CLUS_2           2                67
  CLUS_3           0                36
D8V2, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           2                35
  CLUS_2           1                48
  CLUS_3           0                40
  CLUS_4           0                24
D8V3, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                1                50 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C        TCGA-CU-A0YN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6        TCGA-DK-A1AA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD        TCGA-DK-A1AE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-H4-A2HQ        TCGA-HQ-A2OE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V4, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                1                50 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C        TCGA-CU-A0YN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6        TCGA-DK-A1AA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD        TCGA-DK-A1AE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-H4-A2HQ        TCGA-HQ-A2OE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V5, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           2                53
  CLUS_2           0                23
  CLUS_3           1                44
  CLUS_4           0                25
D8V6, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           0                30
  CLUS_2           2                53
  CLUS_3           1                62
D8V7, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           0                34
  CLUS_2           3                65
  CLUS_3           0                48
D8V8, multiclass
D8V9, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           0                30
  CLUS_2           0                49
  CLUS_3           3                68
D8V10, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           0                25
  CLUS_2           0                36
  CLUS_3           3                86

Clustering(9) Variable = 5p gain
D9V1, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          15                30
  CLUS_2          10                59
  CLUS_3          16                20
D9V2, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           9                28
  CLUS_2          15                34
  CLUS_3          13                27
  CLUS_4           4                20
D9V3, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           5                 6
  CLUS_2           2                 8
  CLUS_3           0                14
  CLUS_4           5                11
D9V4, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           3                10
  CLUS_2           5                 9
  CLUS_3           4                20
D9V5, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          14                41
  CLUS_2           7                16
  CLUS_3          16                29
  CLUS_4           4                21
D9V6, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           4                26
  CLUS_2          17                38
  CLUS_3          20                43
D9V7, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          14                20
  CLUS_2          17                51
  CLUS_3          10                38
D9V8, multiclass
D9V9, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          13                17
  CLUS_2           9                40
  CLUS_3          19                52
D9V10, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          12                13
  CLUS_2           6                30
  CLUS_3          23                66

Clustering(10) Variable = 5q gain
D10V1, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           9                36
  CLUS_2           4                65
  CLUS_3           4                32
D10V2, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           2                35
  CLUS_2           5                44
  CLUS_3           9                31
  CLUS_4           1                23
D10V3, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           1                10
  CLUS_2           0                10
  CLUS_3           0                14
  CLUS_4           3                13
D10V4, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           2                11
  CLUS_2           0                14
  CLUS_3           2                22
D10V5, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           6                49
  CLUS_2           3                20
  CLUS_3           6                39
  CLUS_4           2                23
D10V6, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           3                27
  CLUS_2           6                49
  CLUS_3           8                55
D10V7, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           6                28
  CLUS_2           8                60
  CLUS_3           3                45
D10V8, multiclass
D10V9, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           5                25
  CLUS_2           3                46
  CLUS_3           9                62
D10V10, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           5                20
  CLUS_2           2                34
  CLUS_3          10                79

Clustering(11) Variable = 6p gain
D11V1, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           4                41
  CLUS_2           2                67
  CLUS_3           5                31
D11V2, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           5                32
  CLUS_2           2                47
  CLUS_3           4                36
  CLUS_4           0                24
D11V3, multiclass
[1] "Remove cluster labels:" "6P GAIN CNV"           
clus
      6P GAIN CNV 6P GAIN WILD-TYPE 
                2                49 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AD        TCGA-DK-A1AE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HQ-A2OE 
"6P GAIN WILD-TYPE" 
D11V4, multiclass
[1] "Remove cluster labels:" "6P GAIN CNV"           
clus
      6P GAIN CNV 6P GAIN WILD-TYPE 
                2                49 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AD        TCGA-DK-A1AE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HQ-A2OE 
"6P GAIN WILD-TYPE" 
D11V5, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           3                52
  CLUS_2           3                20
  CLUS_3           4                41
  CLUS_4           1                24
D11V6, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           2                28
  CLUS_2           4                51
  CLUS_3           5                58
D11V7, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           5                29
  CLUS_2           4                64
  CLUS_3           2                46
D11V8, multiclass
D11V9, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           4                26
  CLUS_2           2                47
  CLUS_3           5                66
D11V10, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           5                20
  CLUS_2           2                34
  CLUS_3           4                85

Clustering(12) Variable = 6q gain
D12V1, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1                44
  CLUS_2           1                68
  CLUS_3           4                32
D12V2, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           3                34
  CLUS_2           2                47
  CLUS_3           1                39
  CLUS_4           0                24
D12V3, multiclass
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                2                49 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0        TCGA-C4-A0F6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C        TCGA-CU-A0YN 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6        TCGA-DK-A1AA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A1AB        TCGA-DK-A1AD        TCGA-DK-A1AE        TCGA-DK-A1AF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1        TCGA-DK-A2I2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4        TCGA-G2-A2EF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL        TCGA-G2-A2EO 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HQ-A2OE 
"6Q GAIN WILD-TYPE" 
D12V4, multiclass
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                2                49 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0        TCGA-C4-A0F6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C        TCGA-CU-A0YN 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6        TCGA-DK-A1AA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A1AB        TCGA-DK-A1AD        TCGA-DK-A1AE        TCGA-DK-A1AF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1        TCGA-DK-A2I2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4        TCGA-G2-A2EF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL        TCGA-G2-A2EO 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HQ-A2OE 
"6Q GAIN WILD-TYPE" 
D12V5, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1                54
  CLUS_2           3                20
  CLUS_3           2                43
  CLUS_4           0                25
D12V6, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           0                30
  CLUS_2           2                53
  CLUS_3           4                59
D12V7, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           4                30
  CLUS_2           2                66
  CLUS_3           0                48
D12V8, multiclass
D12V9, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           3                27
  CLUS_2           0                49
  CLUS_3           3                68
D12V10, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           4                21
  CLUS_2           0                36
  CLUS_3           2                87

Clustering(13) Variable = 7p gain
D13V1, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          19                26
  CLUS_2          12                57
  CLUS_3          14                22
D13V2, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          19                18
  CLUS_2          12                37
  CLUS_3          12                28
  CLUS_4           2                22
D13V3, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           3                 8
  CLUS_2           2                 8
  CLUS_3           5                 9
  CLUS_4           6                10
D13V4, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           4                 9
  CLUS_2           2                12
  CLUS_3          10                14
D13V5, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          17                38
  CLUS_2          10                13
  CLUS_3          15                30
  CLUS_4           3                22
D13V6, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           8                22
  CLUS_2          15                40
  CLUS_3          22                41
D13V7, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          12                22
  CLUS_2          26                42
  CLUS_3           7                41
D13V8, multiclass
D13V9, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          11                19
  CLUS_2           9                40
  CLUS_3          25                46
D13V10, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           9                16
  CLUS_2           7                29
  CLUS_3          29                60

Clustering(14) Variable = 7q gain
D14V1, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          18                27
  CLUS_2          10                59
  CLUS_3          13                23
D14V2, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          16                21
  CLUS_2          11                38
  CLUS_3          11                29
  CLUS_4           3                21
D14V3, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           4                 7
  CLUS_2           3                 7
  CLUS_3           5                 9
  CLUS_4           5                11
D14V4, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           3                10
  CLUS_2           3                11
  CLUS_3          11                13
D14V5, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          15                40
  CLUS_2           9                14
  CLUS_3          14                31
  CLUS_4           3                22
D14V6, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           9                21
  CLUS_2          12                43
  CLUS_3          20                43
D14V7, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           9                25
  CLUS_2          22                46
  CLUS_3          10                38
D14V8, multiclass
D14V9, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           8                22
  CLUS_2          12                37
  CLUS_3          21                50
D14V10, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           6                19
  CLUS_2           9                27
  CLUS_3          26                63

Clustering(15) Variable = 8p gain
D15V1, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           8                37
  CLUS_2           7                62
  CLUS_3           0                36
D15V2, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           2                35
  CLUS_2           3                46
  CLUS_3          10                30
  CLUS_4           0                24
D15V3, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           0                11
  CLUS_2           1                 9
  CLUS_3           2                12
  CLUS_4           5                11
D15V4, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           4                 9
  CLUS_2           1                13
  CLUS_3           3                21
D15V5, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           5                50
  CLUS_2           3                20
  CLUS_3           7                38
  CLUS_4           0                25
D15V6, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                29
  CLUS_2           5                50
  CLUS_3           9                54
D15V7, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           3                31
  CLUS_2           8                60
  CLUS_3           4                44
D15V8, multiclass
D15V9, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           3                27
  CLUS_2           3                46
  CLUS_3           9                62
D15V10, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           3                22
  CLUS_2           1                35
  CLUS_3          11                78

Clustering(16) Variable = 8q gain
D16V1, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          22                23
  CLUS_2          16                53
  CLUS_3           6                30
D16V2, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          16                21
  CLUS_2          12                37
  CLUS_3          13                27
  CLUS_4           3                21
D16V3, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           3                 8
  CLUS_2           3                 7
  CLUS_3           3                11
  CLUS_4           7                 9
D16V4, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           6                 7
  CLUS_2           4                10
  CLUS_3           6                18
D16V5, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          19                36
  CLUS_2           9                14
  CLUS_3          13                32
  CLUS_4           3                22
D16V6, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           6                24
  CLUS_2          19                36
  CLUS_3          19                44
D16V7, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          11                23
  CLUS_2          20                48
  CLUS_3          13                35
D16V8, multiclass
D16V9, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          10                20
  CLUS_2          13                36
  CLUS_3          21                50
D16V10, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           9                16
  CLUS_2           8                28
  CLUS_3          27                62

Clustering(17) Variable = 9p gain
D17V1, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           5                40
  CLUS_2           3                66
  CLUS_3           7                29
D17V2, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           6                31
  CLUS_2           4                45
  CLUS_3           4                36
  CLUS_4           1                23
D17V3, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3                 8
  CLUS_2           1                 9
  CLUS_3           0                14
  CLUS_4           2                14
D17V4, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1                12
  CLUS_2           2                12
  CLUS_3           3                21
D17V5, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3                52
  CLUS_2           6                17
  CLUS_3           6                39
  CLUS_4           0                25
D17V6, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1                29
  CLUS_2           2                53
  CLUS_3          12                51
D17V7, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3                31
  CLUS_2          10                58
  CLUS_3           2                46
D17V8, multiclass
D17V9, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3                27
  CLUS_2           1                48
  CLUS_3          11                60
D17V10, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3                22
  CLUS_2           1                35
  CLUS_3          11                78

Clustering(18) Variable = 9q gain
D18V1, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           3                42
  CLUS_2           6                63
  CLUS_3           3                33
D18V2, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           4                33
  CLUS_2           6                43
  CLUS_3           2                38
  CLUS_4           0                24
D18V3, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           4                 7
  CLUS_2           1                 9
  CLUS_3           1                13
  CLUS_4           2                14
D18V4, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1                12
  CLUS_2           4                10
  CLUS_3           3                21
D18V5, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1                54
  CLUS_2           3                20
  CLUS_3           7                38
  CLUS_4           1                24
D18V6, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1                29
  CLUS_2           1                54
  CLUS_3          10                53
D18V7, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           3                31
  CLUS_2           5                63
  CLUS_3           4                44
D18V8, multiclass
D18V9, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                28
  CLUS_2           4                45
  CLUS_3           6                65
D18V10, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                23
  CLUS_2           4                32
  CLUS_3           6                83

Clustering(19) Variable = 10p gain
D19V1, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           16                 29
  CLUS_2            5                 64
  CLUS_3            6                 30
D19V2, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           13                 24
  CLUS_2            6                 43
  CLUS_3            8                 32
  CLUS_4            0                 24
D19V3, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                 10
  CLUS_2            4                  6
  CLUS_3            3                 11
  CLUS_4            5                 11
D19V4, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            4                  9
  CLUS_2            0                 14
  CLUS_3            9                 15
D19V5, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           11                 44
  CLUS_2            4                 19
  CLUS_3            9                 36
  CLUS_4            3                 22
D19V6, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            8                 22
  CLUS_2           11                 44
  CLUS_3            8                 55
D19V7, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            9                 25
  CLUS_2           10                 58
  CLUS_3            8                 40
D19V8, multiclass
D19V9, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            9                 21
  CLUS_2            8                 41
  CLUS_3           10                 61
D19V10, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            6                 19
  CLUS_2            8                 28
  CLUS_3           13                 76

Clustering(20) Variable = 10q gain
D20V1, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            4                 41
  CLUS_2            2                 67
  CLUS_3            1                 35
D20V2, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            4                 33
  CLUS_2            1                 48
  CLUS_3            2                 38
  CLUS_4            0                 24
D20V3, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            2                  8
  CLUS_3            1                 13
  CLUS_4            2                 14
D20V4, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            1                 12
  CLUS_2            0                 14
  CLUS_3            4                 20
D20V5, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            3                 52
  CLUS_2            1                 22
  CLUS_3            1                 44
  CLUS_4            2                 23
D20V6, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            4                 51
  CLUS_3            1                 62
D20V7, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            2                 32
  CLUS_2            2                 66
  CLUS_3            3                 45
D20V8, multiclass
D20V9, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            3                 46
  CLUS_3            2                 69
D20V10, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            1                 24
  CLUS_2            2                 34
  CLUS_3            4                 85

Clustering(21) Variable = 11p gain
D21V1, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            3                 42
  CLUS_2            0                 69
  CLUS_3            4                 32
D21V2, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            1                 36
  CLUS_2            2                 47
  CLUS_3            3                 37
  CLUS_4            1                 23
D21V3, multiclass
[1] "Remove cluster labels:" "11P GAIN CNV"          
clus
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 1                 50 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BT-A0S7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A0YX         TCGA-BT-A20J         TCGA-BT-A20N 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A20O         TCGA-BT-A20P         TCGA-BT-A20Q 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A20R         TCGA-BT-A20T         TCGA-BT-A20U 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A20V         TCGA-BT-A20W         TCGA-BT-A20X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A2LA         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2HX         TCGA-DK-A2I1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A2I2         TCGA-E5-A2PC         TCGA-FD-A3B3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FD-A3B4         TCGA-G2-A2EF         TCGA-G2-A2EJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G2-A2EK         TCGA-G2-A2EL         TCGA-G2-A2EO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G2-A2ES         TCGA-GD-A2C5         TCGA-H4-A2HO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-H4-A2HQ         TCGA-HQ-A2OE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D21V4, multiclass
[1] "Remove cluster labels:" "11P GAIN CNV"          
clus
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 1                 50 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BT-A0S7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A0YX         TCGA-BT-A20J         TCGA-BT-A20N 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A20O         TCGA-BT-A20P         TCGA-BT-A20Q 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A20R         TCGA-BT-A20T         TCGA-BT-A20U 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A20V         TCGA-BT-A20W         TCGA-BT-A20X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BT-A2LA         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2HX         TCGA-DK-A2I1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DK-A2I2         TCGA-E5-A2PC         TCGA-FD-A3B3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FD-A3B4         TCGA-G2-A2EF         TCGA-G2-A2EJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G2-A2EK         TCGA-G2-A2EL         TCGA-G2-A2EO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G2-A2ES         TCGA-GD-A2C5         TCGA-H4-A2HO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-H4-A2HQ         TCGA-HQ-A2OE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D21V5, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            1                 54
  CLUS_2            2                 21
  CLUS_3            4                 41
  CLUS_4            0                 25
D21V6, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            1                 54
  CLUS_3            5                 58
D21V7, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            1                 33
  CLUS_2            5                 63
  CLUS_3            1                 47
D21V8, multiclass
D21V9, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            0                 49
  CLUS_3            6                 65
D21V10, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            0                 25
  CLUS_2            1                 35
  CLUS_3            6                 83

Clustering(22) Variable = 11q gain
D22V1, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            4                 41
  CLUS_2            2                 67
  CLUS_3            3                 33
D22V2, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            3                 34
  CLUS_2            2                 47
  CLUS_3            4                 36
  CLUS_4            0                 24
D22V3, multiclass
[1] "Remove cluster labels:" "11Q GAIN CNV"          
clus
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BT-A0S7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A0YX         TCGA-BT-A20J         TCGA-BT-A20N 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A20O         TCGA-BT-A20P         TCGA-BT-A20Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A20R         TCGA-BT-A20T         TCGA-BT-A20U 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A20V         TCGA-BT-A20W         TCGA-BT-A20X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A2LA         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DK-A1A5         TCGA-DK-A1A6         TCGA-DK-A1AA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DK-A1AB         TCGA-DK-A1AC         TCGA-DK-A1AD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HQ-A2OE 
"11Q GAIN WILD-TYPE" 
D22V4, multiclass
[1] "Remove cluster labels:" "11Q GAIN CNV"          
clus
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BT-A0S7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A0YX         TCGA-BT-A20J         TCGA-BT-A20N 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A20O         TCGA-BT-A20P         TCGA-BT-A20Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A20R         TCGA-BT-A20T         TCGA-BT-A20U 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A20V         TCGA-BT-A20W         TCGA-BT-A20X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BT-A2LA         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DK-A1A5         TCGA-DK-A1A6         TCGA-DK-A1AA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DK-A1AB         TCGA-DK-A1AC         TCGA-DK-A1AD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HQ-A2OE 
"11Q GAIN WILD-TYPE" 
D22V5, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            1                 54
  CLUS_2            2                 21
  CLUS_3            5                 40
  CLUS_4            1                 24
D22V6, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            1                 54
  CLUS_3            6                 57
D22V7, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            2                 32
  CLUS_2            6                 62
  CLUS_3            1                 47
D22V8, multiclass
D22V9, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            1                 48
  CLUS_3            6                 65
D22V10, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            1                 24
  CLUS_2            2                 34
  CLUS_3            6                 83

Clustering(23) Variable = 12p gain
D23V1, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           14                 31
  CLUS_2            7                 62
  CLUS_3            5                 31
D23V2, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            9                 28
  CLUS_2            6                 43
  CLUS_3            8                 32
  CLUS_4            3                 21
D23V3, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            2                  9
  CLUS_2            0                 10
  CLUS_3            1                 13
  CLUS_4            5                 11
D23V4, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            3                 10
  CLUS_2            1                 13
  CLUS_3            4                 20
D23V5, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           11                 44
  CLUS_2            6                 17
  CLUS_3            7                 38
  CLUS_4            2                 23
D23V6, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            1                 29
  CLUS_2           13                 42
  CLUS_3           12                 51
D23V7, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            6                 28
  CLUS_2           14                 54
  CLUS_3            6                 42
D23V8, multiclass
D23V9, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            6                 24
  CLUS_2            4                 45
  CLUS_3           16                 55
D23V10, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            5                 20
  CLUS_2            1                 35
  CLUS_3           20                 69

Clustering(24) Variable = 12q gain
D24V1, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            7                 38
  CLUS_2            8                 61
  CLUS_3            3                 33
D24V2, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            6                 31
  CLUS_2            3                 46
  CLUS_3            7                 33
  CLUS_4            2                 22
D24V3, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            2                  9
  CLUS_2            0                 10
  CLUS_3            2                 12
  CLUS_4            4                 12
D24V4, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            2                 11
  CLUS_2            1                 13
  CLUS_3            5                 19
D24V5, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           10                 45
  CLUS_2            4                 19
  CLUS_3            3                 42
  CLUS_4            1                 24
D24V6, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                 29
  CLUS_2           11                 44
  CLUS_3            6                 57
D24V7, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            7                 27
  CLUS_2            8                 60
  CLUS_3            3                 45
D24V8, multiclass
D24V9, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            7                 23
  CLUS_2            1                 48
  CLUS_3           10                 61
D24V10, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            4                 21
  CLUS_2            1                 35
  CLUS_3           13                 76

Clustering(25) Variable = 13q gain
D25V1, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            6                 39
  CLUS_2            8                 61
  CLUS_3           10                 26
D25V2, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            7                 30
  CLUS_2            9                 40
  CLUS_3            5                 35
  CLUS_4            3                 21
D25V3, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            5                  6
  CLUS_2            1                  9
  CLUS_3            1                 13
  CLUS_4            1                 15
D25V4, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            1                 12
  CLUS_2            5                  9
  CLUS_3            2                 22
D25V5, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            7                 48
  CLUS_2            7                 16
  CLUS_3            3                 42
  CLUS_4            7                 18
D25V6, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            6                 24
  CLUS_2            6                 49
  CLUS_3           12                 51
D25V7, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            4                 30
  CLUS_2            8                 60
  CLUS_3           12                 36
D25V8, multiclass
D25V9, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            4                 26
  CLUS_2           10                 39
  CLUS_3           10                 61
D25V10, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            4                 21
  CLUS_2            6                 30
  CLUS_3           14                 75

Clustering(26) Variable = 14q gain
D26V1, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            2                 43
  CLUS_2            4                 65
  CLUS_3            5                 31
D26V2, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            3                 34
  CLUS_2            4                 45
  CLUS_3            3                 37
  CLUS_4            1                 23
D26V3, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            3                  8
  CLUS_2            0                 10
  CLUS_3            1                 13
  CLUS_4            1                 15
D26V4, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            0                 13
  CLUS_2            2                 12
  CLUS_3            3                 21
D26V5, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            2                 53
  CLUS_2            4                 19
  CLUS_3            4                 41
  CLUS_4            1                 24
D26V6, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            1                 54
  CLUS_3            8                 55
D26V7, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            2                 32
  CLUS_2            7                 61
  CLUS_3            2                 46
D26V8, multiclass
D26V9, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            0                 30
  CLUS_2            3                 46
  CLUS_3            8                 63
D26V10, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            1                 24
  CLUS_2            1                 35
  CLUS_3            9                 80

Clustering(27) Variable = 15q gain
D27V1, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                 44
  CLUS_2            3                 66
  CLUS_3            1                 35
D27V2, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            0                 37
  CLUS_2            0                 49
  CLUS_3            3                 37
  CLUS_4            2                 22
D27V3, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            1                  9
  CLUS_3            2                 12
  CLUS_4            0                 16
D27V4, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            0                 13
  CLUS_2            0                 14
  CLUS_3            3                 21
D27V5, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                 54
  CLUS_2            0                 23
  CLUS_3            1                 44
  CLUS_4            3                 22
D27V6, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            3                 27
  CLUS_2            1                 54
  CLUS_3            1                 62
D27V7, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                 33
  CLUS_2            2                 66
  CLUS_3            2                 46
D27V8, multiclass
D27V9, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            2                 47
  CLUS_3            2                 69
D27V10, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            0                 25
  CLUS_2            3                 33
  CLUS_3            2                 87

Clustering(28) Variable = 16p gain
D28V1, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            3                 42
  CLUS_2            1                 68
  CLUS_3            5                 31
D28V2, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            3                 34
  CLUS_2            2                 47
  CLUS_3            3                 37
  CLUS_4            1                 23
D28V3, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            1                 10
  CLUS_2            1                  9
  CLUS_3            0                 14
  CLUS_4            2                 14
D28V4, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            1                 12
  CLUS_2            1                 13
  CLUS_3            2                 22
D28V5, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            3                 52
  CLUS_2            2                 21
  CLUS_3            4                 41
  CLUS_4            0                 25
D28V6, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            2                 53
  CLUS_3            5                 58
D28V7, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            1                 33
  CLUS_2            4                 64
  CLUS_3            4                 44
D28V8, multiclass
D28V9, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            2                 47
  CLUS_3            6                 65
D28V10, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            0                 25
  CLUS_2            2                 34
  CLUS_3            7                 82

Clustering(29) Variable = 16q gain
D29V1, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            6                 39
  CLUS_2            1                 68
  CLUS_3            6                 30
D29V2, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            5                 32
  CLUS_2            5                 44
  CLUS_3            3                 37
  CLUS_4            0                 24
D29V3, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            1                 10
  CLUS_2            1                  9
  CLUS_3            1                 13
  CLUS_4            2                 14
D29V4, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            1                 12
  CLUS_2            1                 13
  CLUS_3            3                 21
D29V5, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            3                 52
  CLUS_2            4                 19
  CLUS_3            6                 39
  CLUS_4            0                 25
D29V6, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            3                 27
  CLUS_2            2                 53
  CLUS_3            8                 55
D29V7, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            2                 32
  CLUS_2            6                 62
  CLUS_3            5                 43
D29V8, multiclass
D29V9, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            4                 45
  CLUS_3            7                 64
D29V10, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            1                 24
  CLUS_2            3                 33
  CLUS_3            9                 80

Clustering(30) Variable = 17p gain
D30V1, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            4                 41
  CLUS_2            2                 67
  CLUS_3            2                 34
D30V2, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            3                 34
  CLUS_2            2                 47
  CLUS_3            3                 37
  CLUS_4            0                 24
D30V3, multiclass
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 2                 49 
        TCGA-BL-A13I         TCGA-BL-A13J         TCGA-BT-A0S7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A0YX         TCGA-BT-A20J         TCGA-BT-A20N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A20O         TCGA-BT-A20P         TCGA-BT-A20Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A20R         TCGA-BT-A20T         TCGA-BT-A20U 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A20V         TCGA-BT-A20W         TCGA-BT-A20X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A2LA         TCGA-BT-A2LB         TCGA-C4-A0F0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C4-A0F6         TCGA-CF-A1HR         TCGA-CF-A1HS 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CF-A27C         TCGA-CU-A0YN         TCGA-DK-A1A3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DK-A1A5         TCGA-DK-A1A6         TCGA-DK-A1AA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DK-A1AB         TCGA-DK-A1AC         TCGA-DK-A1AD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HQ-A2OE 
"17P GAIN WILD-TYPE" 
D30V4, multiclass
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 2                 49 
        TCGA-BL-A13I         TCGA-BL-A13J         TCGA-BT-A0S7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A0YX         TCGA-BT-A20J         TCGA-BT-A20N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A20O         TCGA-BT-A20P         TCGA-BT-A20Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A20R         TCGA-BT-A20T         TCGA-BT-A20U 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A20V         TCGA-BT-A20W         TCGA-BT-A20X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BT-A2LA         TCGA-BT-A2LB         TCGA-C4-A0F0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C4-A0F6         TCGA-CF-A1HR         TCGA-CF-A1HS 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CF-A27C         TCGA-CU-A0YN         TCGA-DK-A1A3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DK-A1A5         TCGA-DK-A1A6         TCGA-DK-A1AA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DK-A1AB         TCGA-DK-A1AC         TCGA-DK-A1AD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HQ-A2OE 
"17P GAIN WILD-TYPE" 
D30V5, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            3                 52
  CLUS_2            3                 20
  CLUS_3            2                 43
  CLUS_4            0                 25
D30V6, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            0                 30
  CLUS_2            3                 52
  CLUS_3            5                 58
D30V7, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            2                 32
  CLUS_2            4                 64
  CLUS_3            2                 46
D30V8, multiclass
D30V9, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            1                 48
  CLUS_3            5                 66
D30V10, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            1                 24
  CLUS_2            0                 36
  CLUS_3            7                 82

Clustering(31) Variable = 17q gain
D31V1, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           16                 29
  CLUS_2            5                 64
  CLUS_3            3                 33
D31V2, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           10                 27
  CLUS_2            2                 47
  CLUS_3           10                 30
  CLUS_4            2                 22
D31V3, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            3                  8
  CLUS_2            2                  8
  CLUS_3            2                 12
  CLUS_4            1                 15
D31V4, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            0                 13
  CLUS_2            2                 12
  CLUS_3            6                 18
D31V5, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           13                 42
  CLUS_2            7                 16
  CLUS_3            3                 42
  CLUS_4            1                 24
D31V6, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            3                 27
  CLUS_2           14                 41
  CLUS_3            7                 56
D31V7, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            9                 25
  CLUS_2           10                 58
  CLUS_3            5                 43
D31V8, multiclass
D31V9, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            9                 21
  CLUS_2            3                 46
  CLUS_3           12                 59
D31V10, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            7                 18
  CLUS_2            3                 33
  CLUS_3           14                 75

Clustering(32) Variable = 18p gain
D32V1, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1           11                 34
  CLUS_2            2                 67
  CLUS_3           11                 25
D32V2, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            8                 29
  CLUS_2            8                 41
  CLUS_3            8                 32
  CLUS_4            0                 24
D32V3, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                  9
  CLUS_2            0                 10
  CLUS_3            1                 13
  CLUS_4            2                 14
D32V4, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                 11
  CLUS_2            2                 12
  CLUS_3            1                 23
D32V5, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            5                 50
  CLUS_2            8                 15
  CLUS_3           10                 35
  CLUS_4            1                 24
D32V6, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            8                 47
  CLUS_3           14                 49
D32V7, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            7                 27
  CLUS_2           12                 56
  CLUS_3            5                 43
D32V8, multiclass
D32V9, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            6                 24
  CLUS_2            5                 44
  CLUS_3           13                 58
D32V10, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            7                 18
  CLUS_2            2                 34
  CLUS_3           15                 74

Clustering(33) Variable = 18q gain
D33V1, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            5                 40
  CLUS_2            2                 67
  CLUS_3            2                 34
D33V2, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                 35
  CLUS_2            4                 45
  CLUS_3            3                 37
  CLUS_4            0                 24
D33V3, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 10
  CLUS_2            0                 10
  CLUS_3            0                 14
  CLUS_4            2                 14
D33V4, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                 11
  CLUS_2            1                 13
  CLUS_3            0                 24
D33V5, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 54
  CLUS_2            3                 20
  CLUS_3            4                 41
  CLUS_4            1                 24
D33V6, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            1                 54
  CLUS_3            7                 56
D33V7, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 33
  CLUS_2            4                 64
  CLUS_3            4                 44
D33V8, multiclass
D33V9, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            3                 46
  CLUS_3            5                 66
D33V10, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 24
  CLUS_2            1                 35
  CLUS_3            7                 82

Clustering(34) Variable = 19p gain
D34V1, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            5                 40
  CLUS_2            5                 64
  CLUS_3            3                 33
D34V2, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                 35
  CLUS_2            1                 48
  CLUS_3            8                 32
  CLUS_4            2                 22
D34V3, multiclass
[1] "Remove cluster labels:" "19P GAIN CNV"          
clus
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2I1         TCGA-DK-A2I2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HQ-A2OE 
"19P GAIN WILD-TYPE" 
D34V4, multiclass
[1] "Remove cluster labels:" "19P GAIN CNV"          
clus
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2I1         TCGA-DK-A2I2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HQ-A2OE 
"19P GAIN WILD-TYPE" 
D34V5, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            8                 47
  CLUS_2            3                 20
  CLUS_3            1                 44
  CLUS_4            1                 24
D34V6, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            8                 47
  CLUS_3            3                 60
D34V7, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            4                 30
  CLUS_2            6                 62
  CLUS_3            3                 45
D34V8, multiclass
D34V9, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            4                 26
  CLUS_2            1                 48
  CLUS_3            8                 63
D34V10, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            3                 22
  CLUS_2            1                 35
  CLUS_3            9                 80

Clustering(35) Variable = 19q gain
D35V1, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1           14                 31
  CLUS_2            9                 60
  CLUS_3            4                 32
D35V2, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            9                 28
  CLUS_2            5                 44
  CLUS_3            8                 32
  CLUS_4            5                 19
D35V3, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            2                  9
  CLUS_2            1                  9
  CLUS_3            2                 12
  CLUS_4            5                 11
D35V4, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            2                 11
  CLUS_2            3                 11
  CLUS_3            5                 19
D35V5, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1           14                 41
  CLUS_2            6                 17
  CLUS_3            5                 40
  CLUS_4            2                 23
D35V6, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            5                 25
  CLUS_2           13                 42
  CLUS_3            9                 54
D35V7, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            5                 29
  CLUS_2           14                 54
  CLUS_3            8                 40
D35V8, multiclass
D35V9, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            5                 25
  CLUS_2            6                 43
  CLUS_3           16                 55
D35V10, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            4                 21
  CLUS_2            4                 32
  CLUS_3           19                 70

Clustering(36) Variable = 20p gain
D36V1, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           22                 23
  CLUS_2           17                 52
  CLUS_3           15                 21
D36V2, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           16                 21
  CLUS_2           11                 38
  CLUS_3           17                 23
  CLUS_4           10                 14
D36V3, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            6                  5
  CLUS_2            4                  6
  CLUS_3            4                 10
  CLUS_4            4                 12
D36V4, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            4                  9
  CLUS_2            6                  8
  CLUS_3            8                 16
D36V5, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           20                 35
  CLUS_2           11                 12
  CLUS_3           13                 32
  CLUS_4           10                 15
D36V6, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           14                 16
  CLUS_2           20                 35
  CLUS_3           20                 43
D36V7, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           14                 20
  CLUS_2           26                 42
  CLUS_3           14                 34
D36V8, multiclass
D36V9, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           14                 16
  CLUS_2           15                 34
  CLUS_3           25                 46
D36V10, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            9                 16
  CLUS_2           14                 22
  CLUS_3           31                 58

Clustering(37) Variable = 20q gain
D37V1, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           25                 20
  CLUS_2           21                 48
  CLUS_3           14                 22
D37V2, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           18                 19
  CLUS_2           12                 37
  CLUS_3           19                 21
  CLUS_4           11                 13
D37V3, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            6                  5
  CLUS_2            3                  7
  CLUS_3            6                  8
  CLUS_4            4                 12
D37V4, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            3                 10
  CLUS_2            6                  8
  CLUS_3           10                 14
D37V5, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           24                 31
  CLUS_2           14                  9
  CLUS_3           13                 32
  CLUS_4            9                 16
D37V6, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           12                 18
  CLUS_2           26                 29
  CLUS_3           22                 41
D37V7, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           18                 16
  CLUS_2           30                 38
  CLUS_3           12                 36
D37V8, multiclass
D37V9, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           17                 13
  CLUS_2           12                 37
  CLUS_3           31                 40
D37V10, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           13                 12
  CLUS_2           12                 24
  CLUS_3           35                 54

Clustering(38) Variable = 21q gain
D38V1, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           13                 32
  CLUS_2            6                 63
  CLUS_3            8                 28
D38V2, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           15                 22
  CLUS_2            5                 44
  CLUS_3            6                 34
  CLUS_4            1                 23
D38V3, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            3                  8
  CLUS_2            3                  7
  CLUS_3            2                 12
  CLUS_4            2                 14
D38V4, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            1                 12
  CLUS_2            3                 11
  CLUS_3            6                 18
D38V5, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           11                 44
  CLUS_2            7                 16
  CLUS_3            5                 40
  CLUS_4            4                 21
D38V6, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            8                 22
  CLUS_2           12                 43
  CLUS_3            7                 56
D38V7, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            9                 25
  CLUS_2            9                 59
  CLUS_3            9                 39
D38V8, multiclass
D38V9, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            8                 22
  CLUS_2           10                 39
  CLUS_3            9                 62
D38V10, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            7                 18
  CLUS_2           10                 26
  CLUS_3           10                 79

Clustering(39) Variable = 22q gain
D39V1, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            7                 38
  CLUS_2            4                 65
  CLUS_3            1                 35
D39V2, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            3                 34
  CLUS_2            3                 46
  CLUS_3            6                 34
  CLUS_4            0                 24
D39V3, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            0                 10
  CLUS_3            2                 12
  CLUS_4            2                 14
D39V4, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            1                 12
  CLUS_2            0                 14
  CLUS_3            3                 21
D39V5, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            5                 50
  CLUS_2            2                 21
  CLUS_3            5                 40
  CLUS_4            0                 25
D39V6, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            4                 51
  CLUS_3            7                 56
D39V7, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            3                 31
  CLUS_2            9                 59
  CLUS_3            0                 48
D39V8, multiclass
D39V9, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            3                 27
  CLUS_2            0                 49
  CLUS_3            9                 62
D39V10, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            3                 22
  CLUS_2            0                 36
  CLUS_3            9                 80

Clustering(40) Variable = Xq gain
D40V1, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           4                41
  CLUS_2           0                69
  CLUS_3           2                34
D40V2, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           2                35
  CLUS_2           2                47
  CLUS_3           2                38
  CLUS_4           0                24
D40V3, multiclass
[1] "Remove cluster labels:" "XQ GAIN CNV"           
clus
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                1                50 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BT-A0S7        TCGA-BT-A0YX 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O        TCGA-BT-A20P 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T        TCGA-BT-A20U 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X        TCGA-BT-A2LA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0        TCGA-C4-A0F6 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C        TCGA-CU-A0YN 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6        TCGA-DK-A1AA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD        TCGA-DK-A1AE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-H4-A2HQ        TCGA-HQ-A2OE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D40V4, multiclass
[1] "Remove cluster labels:" "XQ GAIN CNV"           
clus
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                1                50 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BT-A0S7        TCGA-BT-A0YX 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O        TCGA-BT-A20P 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T        TCGA-BT-A20U 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X        TCGA-BT-A2LA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0        TCGA-C4-A0F6 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C        TCGA-CU-A0YN 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6        TCGA-DK-A1AA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD        TCGA-DK-A1AE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-H4-A2HQ        TCGA-HQ-A2OE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D40V5, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           1                54
  CLUS_2           3                20
  CLUS_3           2                43
  CLUS_4           0                25
D40V6, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           1                29
  CLUS_2           3                52
  CLUS_3           2                61
D40V7, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           2                32
  CLUS_2           3                65
  CLUS_3           1                47
D40V8, multiclass
D40V9, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           2                28
  CLUS_2           1                48
  CLUS_3           3                68
D40V10, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           1                24
  CLUS_2           1                35
  CLUS_3           4                85

Clustering(41) Variable = 1p loss
D41V1, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           3                42
  CLUS_2           1                68
  CLUS_3           0                36
D41V2, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           0                37
  CLUS_2           0                49
  CLUS_3           2                38
  CLUS_4           2                22
D41V3, multiclass
D41V4, multiclass
D41V5, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           3                52
  CLUS_2           1                22
  CLUS_3           0                45
  CLUS_4           0                25
D41V6, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           0                30
  CLUS_2           3                52
  CLUS_3           1                62
D41V7, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1                33
  CLUS_2           3                65
  CLUS_3           0                48
D41V8, multiclass
D41V9, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1                29
  CLUS_2           0                49
  CLUS_3           3                68
D41V10, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           0                25
  CLUS_2           0                36
  CLUS_3           4                85

Clustering(42) Variable = 2p loss
D42V1, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           3                42
  CLUS_2           2                67
  CLUS_3           3                33
D42V2, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                37
  CLUS_2           1                48
  CLUS_3           3                37
  CLUS_4           4                20
D42V3, multiclass
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                2                49 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DK-A1AE        TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2I1 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HQ-A2OE 
"2P LOSS WILD-TYPE" 
D42V4, multiclass
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                2                49 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DK-A1AE        TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2I1 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO        TCGA-H4-A2HQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HQ-A2OE 
"2P LOSS WILD-TYPE" 
D42V5, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           6                49
  CLUS_2           1                22
  CLUS_3           0                45
  CLUS_4           1                24
D42V6, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2                28
  CLUS_2           5                50
  CLUS_3           1                62
D42V7, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2                32
  CLUS_2           4                64
  CLUS_3           2                46
D42V8, multiclass
D42V9, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2                28
  CLUS_2           1                48
  CLUS_3           5                66
D42V10, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1                24
  CLUS_2           1                35
  CLUS_3           6                83

Clustering(43) Variable = 2q loss
D43V1, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1          10                35
  CLUS_2           3                66
  CLUS_3           4                32
D43V2, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           5                32
  CLUS_2           3                46
  CLUS_3           6                34
  CLUS_4           3                21
D43V3, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1                10
  CLUS_2           1                 9
  CLUS_3           1                13
  CLUS_4           2                14
D43V4, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1                12
  CLUS_2           0                14
  CLUS_3           4                20
D43V5, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           9                46
  CLUS_2           4                19
  CLUS_3           2                43
  CLUS_4           2                23
D43V6, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           4                26
  CLUS_2           8                47
  CLUS_3           5                58
D43V7, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           4                30
  CLUS_2           8                60
  CLUS_3           5                43
D43V8, multiclass
D43V9, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           4                26
  CLUS_2           4                45
  CLUS_3           9                62
D43V10, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           3                22
  CLUS_2           3                33
  CLUS_3          11                78

Clustering(44) Variable = 3p loss
D44V1, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           4                41
  CLUS_2           3                66
  CLUS_3           2                34
D44V2, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           1                36
  CLUS_2           4                45
  CLUS_3           3                37
  CLUS_4           1                23
D44V3, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                11
  CLUS_2           0                10
  CLUS_3           1                13
  CLUS_4           3                13
D44V4, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           2                11
  CLUS_2           1                13
  CLUS_3           1                23
D44V5, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           1                54
  CLUS_2           1                22
  CLUS_3           7                38
  CLUS_4           0                25
D44V6, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                30
  CLUS_2           2                53
  CLUS_3           7                56
D44V7, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                34
  CLUS_2           6                62
  CLUS_3           3                45
D44V8, multiclass
D44V9, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                30
  CLUS_2           3                46
  CLUS_3           6                65
D44V10, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                25
  CLUS_2           2                34
  CLUS_3           7                82

Clustering(45) Variable = 4p loss
D45V1, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          15                30
  CLUS_2           7                62
  CLUS_3           7                29
D45V2, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          10                27
  CLUS_2           5                44
  CLUS_3          10                30
  CLUS_4           4                20
D45V3, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           1                10
  CLUS_2           1                 9
  CLUS_3           3                11
  CLUS_4           2                14
D45V4, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           2                11
  CLUS_2           1                13
  CLUS_3           4                20
D45V5, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          10                45
  CLUS_2           6                17
  CLUS_3           9                36
  CLUS_4           3                22
D45V6, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           6                24
  CLUS_2          12                43
  CLUS_3          10                53
D45V7, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           6                28
  CLUS_2          16                52
  CLUS_3           7                41
D45V8, multiclass
D45V9, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           3                27
  CLUS_2           9                40
  CLUS_3          17                54
D45V10, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           4                21
  CLUS_2           6                30
  CLUS_3          19                70

Clustering(46) Variable = 4q loss
D46V1, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          14                31
  CLUS_2           7                62
  CLUS_3           6                30
D46V2, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           9                28
  CLUS_2           8                41
  CLUS_3           7                33
  CLUS_4           3                21
D46V3, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                 9
  CLUS_2           2                 8
  CLUS_3           3                11
  CLUS_4           2                14
D46V4, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                11
  CLUS_2           2                12
  CLUS_3           5                19
D46V5, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           8                47
  CLUS_2           6                17
  CLUS_3           9                36
  CLUS_4           3                22
D46V6, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           6                24
  CLUS_2           9                46
  CLUS_3          11                52
D46V7, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           5                29
  CLUS_2          15                53
  CLUS_3           7                41
D46V8, multiclass
D46V9, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                28
  CLUS_2          10                39
  CLUS_3          15                56
D46V10, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           3                22
  CLUS_2           7                29
  CLUS_3          17                72

Clustering(47) Variable = 5p loss
D47V1, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1          10                35
  CLUS_2           3                66
  CLUS_3           1                35
D47V2, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           7                30
  CLUS_2           3                46
  CLUS_3           2                38
  CLUS_4           2                22
D47V3, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1                10
  CLUS_2           0                10
  CLUS_3           3                11
  CLUS_4           1                15
D47V4, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1                12
  CLUS_2           1                13
  CLUS_3           3                21
D47V5, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           8                47
  CLUS_2           2                21
  CLUS_3           3                42
  CLUS_4           1                24
D47V6, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2                28
  CLUS_2           9                46
  CLUS_3           3                60
D47V7, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2                32
  CLUS_2          10                58
  CLUS_3           2                46
D47V8, multiclass
D47V9, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1                29
  CLUS_2           3                46
  CLUS_3          10                61
D47V10, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1                24
  CLUS_2           2                34
  CLUS_3          11                78

Clustering(48) Variable = 5q loss
D48V1, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          19                26
  CLUS_2           6                63
  CLUS_3          10                26
D48V2, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          14                23
  CLUS_2           9                40
  CLUS_3           9                31
  CLUS_4           3                21
D48V3, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           2                 9
  CLUS_2           1                 9
  CLUS_3           4                10
  CLUS_4           2                14
D48V4, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           2                11
  CLUS_2           2                12
  CLUS_3           5                19
D48V5, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          11                44
  CLUS_2           7                16
  CLUS_3          12                33
  CLUS_4           3                22
D48V6, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           6                24
  CLUS_2          15                40
  CLUS_3          12                51
D48V7, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          10                24
  CLUS_2          18                50
  CLUS_3           7                41
D48V8, multiclass
D48V9, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           7                23
  CLUS_2           9                40
  CLUS_3          19                52
D48V10, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           7                18
  CLUS_2           6                30
  CLUS_3          22                67

Clustering(49) Variable = 6p loss
D49V1, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          10                35
  CLUS_2           6                63
  CLUS_3           4                32
D49V2, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           8                29
  CLUS_2           3                46
  CLUS_3           4                36
  CLUS_4           5                19
D49V3, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           0                11
  CLUS_2           0                10
  CLUS_3           3                11
  CLUS_4           3                13
D49V4, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           3                10
  CLUS_2           1                13
  CLUS_3           2                22
D49V5, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           7                48
  CLUS_2           5                18
  CLUS_3           5                40
  CLUS_4           2                23
D49V6, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           4                26
  CLUS_2           8                47
  CLUS_3           7                56
D49V7, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           4                30
  CLUS_2           8                60
  CLUS_3           8                40
D49V8, multiclass
D49V9, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           2                28
  CLUS_2           9                40
  CLUS_3           9                62
D49V10, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           3                22
  CLUS_2           6                30
  CLUS_3          11                78

Clustering(50) Variable = 6q loss
D50V1, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          18                27
  CLUS_2           7                62
  CLUS_3           4                32
D50V2, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          12                25
  CLUS_2           3                46
  CLUS_3           8                32
  CLUS_4           6                18
D50V3, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           1                10
  CLUS_2           0                10
  CLUS_3           4                10
  CLUS_4           4                12
D50V4, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           3                10
  CLUS_2           2                12
  CLUS_3           4                20
D50V5, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          12                43
  CLUS_2           7                16
  CLUS_3           6                39
  CLUS_4           3                22
D50V6, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           5                25
  CLUS_2          15                40
  CLUS_3           8                55
D50V7, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           7                27
  CLUS_2          15                53
  CLUS_3           7                41
D50V8, multiclass
D50V9, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           5                25
  CLUS_2           9                40
  CLUS_3          15                56
D50V10, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           5                20
  CLUS_2           7                29
  CLUS_3          17                72

Clustering(51) Variable = 7q loss
D51V1, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           2                43
  CLUS_2           1                68
  CLUS_3           0                36
D51V2, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           1                36
  CLUS_2           0                49
  CLUS_3           2                38
  CLUS_4           0                24
D51V3, multiclass
[1] "Remove cluster labels:" "7Q LOSS CNV"           
clus
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                1                50 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-DK-A1A3        TCGA-DK-A1A6        TCGA-DK-A1AA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD        TCGA-DK-A1AE 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-H4-A2HQ        TCGA-HQ-A2OE 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
D51V4, multiclass
[1] "Remove cluster labels:" "7Q LOSS CNV"           
clus
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                1                50 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-DK-A1A3        TCGA-DK-A1A6        TCGA-DK-A1AA 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD        TCGA-DK-A1AE 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX        TCGA-DK-A2I1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3        TCGA-FD-A3B4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK        TCGA-G2-A2EL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-GD-A2C5        TCGA-H4-A2HO 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-H4-A2HQ        TCGA-HQ-A2OE 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
D51V5, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           2                53
  CLUS_2           0                23
  CLUS_3           0                45
  CLUS_4           1                24
D51V6, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           1                29
  CLUS_2           2                53
  CLUS_3           0                63
D51V7, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           2                32
  CLUS_2           1                67
  CLUS_3           0                48
D51V8, multiclass
D51V9, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           2                28
  CLUS_2           0                49
  CLUS_3           1                70
D51V10, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           1                24
  CLUS_2           1                35
  CLUS_3           1                88

Clustering(52) Variable = 8p loss
D52V1, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          18                27
  CLUS_2           7                62
  CLUS_3          23                13
D52V2, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          24                13
  CLUS_2          14                35
  CLUS_3           5                35
  CLUS_4           5                19
D52V3, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           5                 6
  CLUS_2           4                 6
  CLUS_3           2                12
  CLUS_4           2                14
D52V4, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           2                11
  CLUS_2           6                 8
  CLUS_3           5                19
D52V5, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          15                40
  CLUS_2          12                11
  CLUS_3          13                32
  CLUS_4           8                17
D52V6, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          12                18
  CLUS_2          17                38
  CLUS_3          19                44
D52V7, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          18                16
  CLUS_2          17                51
  CLUS_3          13                35
D52V8, multiclass
D52V9, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          14                16
  CLUS_2          14                35
  CLUS_3          20                51
D52V10, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          14                11
  CLUS_2          12                24
  CLUS_3          22                67

Clustering(53) Variable = 8q loss
D53V1, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           3                42
  CLUS_2           1                68
  CLUS_3           2                34
D53V2, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           4                33
  CLUS_2           2                47
  CLUS_3           0                40
  CLUS_4           0                24
D53V3, multiclass
[1] "Remove cluster labels:" "8Q LOSS CNV"           
clus
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                1                50 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DK-A1AE        TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DK-A2I1        TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FD-A3B4        TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G2-A2EL        TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-GD-A2C5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-H4-A2HO        TCGA-HQ-A2OE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D53V4, multiclass
[1] "Remove cluster labels:" "8Q LOSS CNV"           
clus
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                1                50 
       TCGA-BL-A0C8        TCGA-BL-A13I        TCGA-BL-A13J        TCGA-BT-A0S7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BT-A0YX        TCGA-BT-A20J        TCGA-BT-A20N        TCGA-BT-A20O 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BT-A20P        TCGA-BT-A20Q        TCGA-BT-A20R        TCGA-BT-A20T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BT-A20U        TCGA-BT-A20V        TCGA-BT-A20W        TCGA-BT-A20X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BT-A2LA        TCGA-BT-A2LB        TCGA-C4-A0EZ        TCGA-C4-A0F0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-C4-A0F6        TCGA-CF-A1HR        TCGA-CF-A1HS        TCGA-CF-A27C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CU-A0YN        TCGA-DK-A1A3        TCGA-DK-A1A5        TCGA-DK-A1A6 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DK-A1AA        TCGA-DK-A1AB        TCGA-DK-A1AC        TCGA-DK-A1AD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DK-A1AE        TCGA-DK-A1AF        TCGA-DK-A1AG        TCGA-DK-A2HX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DK-A2I1        TCGA-DK-A2I2        TCGA-E5-A2PC        TCGA-FD-A3B3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FD-A3B4        TCGA-G2-A2EF        TCGA-G2-A2EJ        TCGA-G2-A2EK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G2-A2EL        TCGA-G2-A2EO        TCGA-G2-A2ES        TCGA-GD-A2C5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-H4-A2HO        TCGA-HQ-A2OE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D53V5, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           1                54
  CLUS_2           2                21
  CLUS_3           1                44
  CLUS_4           2                23
D53V6, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           3                27
  CLUS_2           2                53
  CLUS_3           1                62
D53V7, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           3                31
  CLUS_2           1                67
  CLUS_3           2                46
D53V8, multiclass
D53V9, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           3                27
  CLUS_2           2                47
  CLUS_3           1                70
D53V10, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           3                22
  CLUS_2           2                34
  CLUS_3           1                88

Clustering(54) Variable = 9p loss
D54V1, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          15                30
  CLUS_2          27                42
  CLUS_3           1                35
D54V2, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          11                26
  CLUS_2           5                44
  CLUS_3          18                22
  CLUS_4           9                15
D54V3, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           0                11
  CLUS_2           3                 7
  CLUS_3          10                 4
  CLUS_4           5                11
D54V4, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           3                10
  CLUS_2           3                11
  CLUS_3          12                12
D54V5, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          24                31
  CLUS_2           2                21
  CLUS_3           9                36
  CLUS_4           7                18
D54V6, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          11                19
  CLUS_2          24                31
  CLUS_3           7                56
D54V7, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           9                25
  CLUS_2          21                47
  CLUS_3          13                35
D54V8, multiclass
D54V9, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           7                23
  CLUS_2          14                35
  CLUS_3          22                49
D54V10, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           5                20
  CLUS_2          12                24
  CLUS_3          26                63

Clustering(55) Variable = 9q loss
D55V1, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          15                30
  CLUS_2          22                47
  CLUS_3           4                32
D55V2, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          10                27
  CLUS_2           5                44
  CLUS_3          18                22
  CLUS_4           8                16
D55V3, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           2                 9
  CLUS_2           0                10
  CLUS_3          10                 4
  CLUS_4           5                11
D55V4, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           3                10
  CLUS_2           1                13
  CLUS_3          13                11
D55V5, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          26                29
  CLUS_2           3                20
  CLUS_3           5                40
  CLUS_4           6                19
D55V6, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          13                17
  CLUS_2          23                32
  CLUS_3           4                59
D55V7, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          10                24
  CLUS_2          19                49
  CLUS_3          12                36
D55V8, multiclass
D55V9, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           9                21
  CLUS_2          12                37
  CLUS_3          20                51
D55V10, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           7                18
  CLUS_2          11                25
  CLUS_3          23                66

Clustering(56) Variable = 10p loss
D56V1, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            9                 36
  CLUS_2            3                 66
  CLUS_3            7                 29
D56V2, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            5                 32
  CLUS_2            6                 43
  CLUS_3            6                 34
  CLUS_4            2                 22
D56V3, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            3                  8
  CLUS_2            1                  9
  CLUS_3            0                 14
  CLUS_4            2                 14
D56V4, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                 12
  CLUS_2            3                 11
  CLUS_3            2                 22
D56V5, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            4                 51
  CLUS_2            6                 17
  CLUS_3            7                 38
  CLUS_4            2                 23
D56V6, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            7                 48
  CLUS_3           11                 52
D56V7, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            5                 29
  CLUS_2           11                 57
  CLUS_3            3                 45
D56V8, multiclass
D56V9, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            5                 25
  CLUS_2            3                 46
  CLUS_3           11                 60
D56V10, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            4                 21
  CLUS_2            3                 33
  CLUS_3           12                 77

Clustering(57) Variable = 10q loss
D57V1, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           17                 28
  CLUS_2            5                 64
  CLUS_3            8                 28
D57V2, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           12                 25
  CLUS_2            5                 44
  CLUS_3            9                 31
  CLUS_4            4                 20
D57V3, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                 10
  CLUS_2            1                  9
  CLUS_3            2                 12
  CLUS_4            1                 15
D57V4, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                 12
  CLUS_2            2                 12
  CLUS_3            2                 22
D57V5, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           12                 43
  CLUS_2            6                 17
  CLUS_3            8                 37
  CLUS_4            3                 22
D57V6, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            3                 27
  CLUS_2           16                 39
  CLUS_3           10                 53
D57V7, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           10                 24
  CLUS_2           16                 52
  CLUS_3            4                 44
D57V8, multiclass
D57V9, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           10                 20
  CLUS_2            5                 44
  CLUS_3           15                 56
D57V10, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            8                 17
  CLUS_2            5                 31
  CLUS_3           17                 72

Clustering(58) Variable = 11p loss
D58V1, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           24                 21
  CLUS_2           15                 54
  CLUS_3            8                 28
D58V2, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           12                 25
  CLUS_2            6                 43
  CLUS_3           20                 20
  CLUS_4            9                 15
D58V3, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            2                  9
  CLUS_2            3                  7
  CLUS_3            8                  6
  CLUS_4            6                 10
D58V4, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            5                  8
  CLUS_2            4                 10
  CLUS_3           10                 14
D58V5, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           25                 30
  CLUS_2            4                 19
  CLUS_3           12                 33
  CLUS_4            5                 20
D58V6, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           11                 19
  CLUS_2           24                 31
  CLUS_3           11                 52
D58V7, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           14                 20
  CLUS_2           23                 45
  CLUS_3           10                 38
D58V8, multiclass
D58V9, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           11                 19
  CLUS_2           14                 35
  CLUS_3           22                 49
D58V10, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            9                 16
  CLUS_2           12                 24
  CLUS_3           26                 63

Clustering(59) Variable = 11q loss
D59V1, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1           17                 28
  CLUS_2           10                 59
  CLUS_3            7                 29
D59V2, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            7                 30
  CLUS_2            8                 41
  CLUS_3           16                 24
  CLUS_4            3                 21
D59V3, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                 10
  CLUS_2            2                  8
  CLUS_3            5                  9
  CLUS_4            8                  8
D59V4, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            6                  7
  CLUS_2            3                 11
  CLUS_3            7                 17
D59V5, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1           18                 37
  CLUS_2            3                 20
  CLUS_3           11                 34
  CLUS_4            1                 24
D59V6, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            5                 25
  CLUS_2           17                 38
  CLUS_3           11                 52
D59V7, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            8                 26
  CLUS_2           19                 49
  CLUS_3            7                 41
D59V8, multiclass
D59V9, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            8                 22
  CLUS_2            8                 41
  CLUS_3           18                 53
D59V10, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            6                 19
  CLUS_2            6                 30
  CLUS_3           22                 67

Clustering(60) Variable = 12p loss
D60V1, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            2                 43
  CLUS_2            2                 67
  CLUS_3            2                 34
D60V2, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            3                 34
  CLUS_2            0                 49
  CLUS_3            2                 38
  CLUS_4            1                 23
D60V3, multiclass
[1] "Remove cluster labels:" "12P LOSS CNV"          
clus
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 1                 50 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2HX         TCGA-DK-A2I1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A2I2         TCGA-E5-A2PC         TCGA-FD-A3B3 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FD-A3B4         TCGA-G2-A2EF         TCGA-G2-A2EJ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G2-A2EK         TCGA-G2-A2EL         TCGA-G2-A2EO 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G2-A2ES         TCGA-GD-A2C5         TCGA-H4-A2HO 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-H4-A2HQ         TCGA-HQ-A2OE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D60V4, multiclass
[1] "Remove cluster labels:" "12P LOSS CNV"          
clus
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 1                 50 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2HX         TCGA-DK-A2I1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DK-A2I2         TCGA-E5-A2PC         TCGA-FD-A3B3 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FD-A3B4         TCGA-G2-A2EF         TCGA-G2-A2EJ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G2-A2EK         TCGA-G2-A2EL         TCGA-G2-A2EO 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G2-A2ES         TCGA-GD-A2C5         TCGA-H4-A2HO 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-H4-A2HQ         TCGA-HQ-A2OE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D60V5, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            4                 51
  CLUS_2            1                 22
  CLUS_3            0                 45
  CLUS_4            1                 24
D60V6, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            4                 51
  CLUS_3            1                 62
D60V7, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                 33
  CLUS_2            4                 64
  CLUS_3            1                 47
D60V8, multiclass
D60V9, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            1                 48
  CLUS_3            4                 67
D60V10, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                 24
  CLUS_2            1                 35
  CLUS_3            4                 85

Clustering(61) Variable = 12q loss
D61V1, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            1                 44
  CLUS_2            3                 66
  CLUS_3            3                 33
D61V2, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            1                 36
  CLUS_2            2                 47
  CLUS_3            3                 37
  CLUS_4            1                 23
D61V3, multiclass
[1] "Remove cluster labels:" "12Q LOSS CNV"          
clus
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 1                 50 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LA         TCGA-BT-A2LB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C4-A0EZ         TCGA-C4-A0F6         TCGA-CF-A1HR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2HX         TCGA-DK-A2I1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A2I2         TCGA-E5-A2PC         TCGA-FD-A3B3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FD-A3B4         TCGA-G2-A2EF         TCGA-G2-A2EJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G2-A2EK         TCGA-G2-A2EL         TCGA-G2-A2EO 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G2-A2ES         TCGA-GD-A2C5         TCGA-H4-A2HO 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-H4-A2HQ         TCGA-HQ-A2OE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
D61V4, multiclass
[1] "Remove cluster labels:" "12Q LOSS CNV"          
clus
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 1                 50 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LA         TCGA-BT-A2LB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C4-A0EZ         TCGA-C4-A0F6         TCGA-CF-A1HR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2HX         TCGA-DK-A2I1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DK-A2I2         TCGA-E5-A2PC         TCGA-FD-A3B3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FD-A3B4         TCGA-G2-A2EF         TCGA-G2-A2EJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G2-A2EK         TCGA-G2-A2EL         TCGA-G2-A2EO 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G2-A2ES         TCGA-GD-A2C5         TCGA-H4-A2HO 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-H4-A2HQ         TCGA-HQ-A2OE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
D61V5, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            4                 51
  CLUS_2            0                 23
  CLUS_3            3                 42
  CLUS_4            0                 25
D61V6, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            0                 30
  CLUS_2            4                 51
  CLUS_3            3                 60
D61V7, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            2                 32
  CLUS_2            4                 64
  CLUS_3            1                 47
D61V8, multiclass
D61V9, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            1                 48
  CLUS_3            4                 67
D61V10, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            2                 23
  CLUS_2            1                 35
  CLUS_3            4                 85

Clustering(62) Variable = 13q loss
D62V1, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           10                 35
  CLUS_2            8                 61
  CLUS_3            2                 34
D62V2, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            5                 32
  CLUS_2            6                 43
  CLUS_3            8                 32
  CLUS_4            1                 23
D62V3, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            2                  8
  CLUS_3            2                 12
  CLUS_4            6                 10
D62V4, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            5                  8
  CLUS_2            1                 13
  CLUS_3            4                 20
D62V5, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            4                 51
  CLUS_2            4                 19
  CLUS_3           10                 35
  CLUS_4            2                 23
D62V6, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            6                 49
  CLUS_3           12                 51
D62V7, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            6                 28
  CLUS_2            9                 59
  CLUS_3            5                 43
D62V8, multiclass
D62V9, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            5                 25
  CLUS_2            6                 43
  CLUS_3            9                 62
D62V10, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            4                 21
  CLUS_2            3                 33
  CLUS_3           13                 76

Clustering(63) Variable = 14q loss
D63V1, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           12                 33
  CLUS_2            7                 62
  CLUS_3            6                 30
D63V2, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           12                 25
  CLUS_2            5                 44
  CLUS_3            6                 34
  CLUS_4            2                 22
D63V3, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            1                 10
  CLUS_2            2                  8
  CLUS_3            3                 11
  CLUS_4            4                 12
D63V4, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            4                  9
  CLUS_2            1                 13
  CLUS_3            5                 19
D63V5, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           11                 44
  CLUS_2            6                 17
  CLUS_3            5                 40
  CLUS_4            3                 22
D63V6, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            6                 24
  CLUS_2           11                 44
  CLUS_3            8                 55
D63V7, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           11                 23
  CLUS_2            8                 60
  CLUS_3            6                 42
D63V8, multiclass
D63V9, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            8                 22
  CLUS_2            9                 40
  CLUS_3            8                 63
D63V10, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            6                 19
  CLUS_2            6                 30
  CLUS_3           13                 76

Clustering(64) Variable = 15q loss
D64V1, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            8                 37
  CLUS_2            5                 64
  CLUS_3            6                 30
D64V2, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            6                 31
  CLUS_2            9                 40
  CLUS_3            4                 36
  CLUS_4            0                 24
D64V3, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            4                  7
  CLUS_2            0                 10
  CLUS_3            1                 13
  CLUS_4            3                 13
D64V4, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            3                 10
  CLUS_2            3                 11
  CLUS_3            2                 22
D64V5, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            5                 50
  CLUS_2            4                 19
  CLUS_3            9                 36
  CLUS_4            0                 25
D64V6, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            7                 48
  CLUS_3           10                 53
D64V7, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            3                 31
  CLUS_2           13                 55
  CLUS_3            3                 45
D64V8, multiclass
D64V9, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            5                 44
  CLUS_3           12                 59
D64V10, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            2                 23
  CLUS_2            1                 35
  CLUS_3           16                 73

Clustering(65) Variable = 16p loss
D65V1, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            6                 39
  CLUS_2            1                 68
  CLUS_3           10                 26
D65V2, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            7                 30
  CLUS_2            6                 43
  CLUS_3            3                 37
  CLUS_4            1                 23
D65V3, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            2                  9
  CLUS_2            2                  8
  CLUS_3            1                 13
  CLUS_4            1                 15
D65V4, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            1                 12
  CLUS_2            2                 12
  CLUS_3            3                 21
D65V5, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            2                 53
  CLUS_2            6                 17
  CLUS_3            7                 38
  CLUS_4            2                 23
D65V6, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            5                 50
  CLUS_3           10                 53
D65V7, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            4                 30
  CLUS_2           11                 57
  CLUS_3            2                 46
D65V8, multiclass
D65V9, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            4                 26
  CLUS_2            2                 47
  CLUS_3           11                 60
D65V10, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            4                 21
  CLUS_2            2                 34
  CLUS_3           11                 78

Clustering(66) Variable = 16q loss
D66V1, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            6                 39
  CLUS_2            1                 68
  CLUS_3           10                 26
D66V2, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            8                 29
  CLUS_2            3                 46
  CLUS_3            4                 36
  CLUS_4            2                 22
D66V3, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            1                 10
  CLUS_2            2                  8
  CLUS_3            1                 13
  CLUS_4            1                 15
D66V4, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            1                 12
  CLUS_2            1                 13
  CLUS_3            3                 21
D66V5, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            3                 52
  CLUS_2            7                 16
  CLUS_3            5                 40
  CLUS_4            2                 23
D66V6, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            6                 49
  CLUS_3            9                 54
D66V7, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            5                 29
  CLUS_2            8                 60
  CLUS_3            4                 44
D66V8, multiclass
D66V9, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            5                 25
  CLUS_2            3                 46
  CLUS_3            9                 62
D66V10, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            5                 20
  CLUS_2            2                 34
  CLUS_3           10                 79

Clustering(67) Variable = 17p loss
D67V1, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           14                 31
  CLUS_2           21                 48
  CLUS_3            8                 28
D67V2, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            9                 28
  CLUS_2           11                 38
  CLUS_3           11                 29
  CLUS_4           12                 12
D67V3, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            5                  6
  CLUS_2            2                  8
  CLUS_3            4                 10
  CLUS_4            7                  9
D67V4, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            4                  9
  CLUS_2            6                  8
  CLUS_3            8                 16
D67V5, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           22                 33
  CLUS_2            5                 18
  CLUS_3           13                 32
  CLUS_4            2                 23
D67V6, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            9                 21
  CLUS_2           19                 36
  CLUS_3           14                 49
D67V7, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            5                 29
  CLUS_2           24                 44
  CLUS_3           14                 34
D67V8, multiclass
D67V9, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            3                 27
  CLUS_2           14                 35
  CLUS_3           26                 45
D67V10, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            3                 22
  CLUS_2           12                 24
  CLUS_3           28                 61

Clustering(68) Variable = 17q loss
D68V1, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            3                 42
  CLUS_2            2                 67
  CLUS_3            1                 35
D68V2, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            2                 35
  CLUS_2            0                 49
  CLUS_3            1                 39
  CLUS_4            3                 21
D68V3, multiclass
[1] "Remove cluster labels:" "17Q LOSS CNV"          
clus
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AC         TCGA-DK-A1AD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HQ-A2OE 
"17Q LOSS WILD-TYPE" 
D68V4, multiclass
[1] "Remove cluster labels:" "17Q LOSS CNV"          
clus
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AC         TCGA-DK-A1AD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HQ-A2OE 
"17Q LOSS WILD-TYPE" 
D68V5, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            4                 51
  CLUS_2            1                 22
  CLUS_3            1                 44
  CLUS_4            0                 25
D68V6, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            0                 30
  CLUS_2            4                 51
  CLUS_3            2                 61
D68V7, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            0                 34
  CLUS_2            5                 63
  CLUS_3            1                 47
D68V8, multiclass
D68V9, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            0                 30
  CLUS_2            1                 48
  CLUS_3            5                 66
D68V10, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            0                 25
  CLUS_2            1                 35
  CLUS_3            5                 84

Clustering(69) Variable = 18p loss
D69V1, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            8                 37
  CLUS_2           12                 57
  CLUS_3            1                 35
D69V2, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            5                 32
  CLUS_2            2                 47
  CLUS_3            9                 31
  CLUS_4            5                 19
D69V3, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            1                  9
  CLUS_3            2                 12
  CLUS_4            3                 13
D69V4, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            3                 10
  CLUS_2            1                 13
  CLUS_3            2                 22
D69V5, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            8                 47
  CLUS_2            2                 21
  CLUS_3            5                 40
  CLUS_4            4                 21
D69V6, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            5                 25
  CLUS_2           10                 45
  CLUS_3            4                 59
D69V7, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            3                 31
  CLUS_2           12                 56
  CLUS_3            6                 42
D69V8, multiclass
D69V9, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            0                 30
  CLUS_2           10                 39
  CLUS_3           11                 60
D69V10, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            0                 25
  CLUS_2            7                 29
  CLUS_3           14                 75

Clustering(70) Variable = 18q loss
D70V1, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           14                 31
  CLUS_2           11                 58
  CLUS_3           12                 24
D70V2, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           12                 25
  CLUS_2            9                 40
  CLUS_3           10                 30
  CLUS_4            6                 18
D70V3, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            3                  8
  CLUS_2            2                  8
  CLUS_3            2                 12
  CLUS_4            4                 12
D70V4, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            4                  9
  CLUS_2            5                  9
  CLUS_3            2                 22
D70V5, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           14                 41
  CLUS_2            6                 17
  CLUS_3           12                 33
  CLUS_4            3                 22
D70V6, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            4                 26
  CLUS_2           19                 36
  CLUS_3           12                 51
D70V7, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           12                 22
  CLUS_2           16                 52
  CLUS_3            9                 39
D70V8, multiclass
D70V9, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            8                 22
  CLUS_2           13                 36
  CLUS_3           16                 55
D70V10, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            8                 17
  CLUS_2            7                 29
  CLUS_3           22                 67

Clustering(71) Variable = 19p loss
D71V1, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            4                 41
  CLUS_2            1                 68
  CLUS_3            4                 32
D71V2, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            2                 35
  CLUS_2            4                 45
  CLUS_3            2                 38
  CLUS_4            1                 23
D71V3, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            2                  9
  CLUS_2            0                 10
  CLUS_3            0                 14
  CLUS_4            1                 15
D71V4, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                 12
  CLUS_2            2                 12
  CLUS_3            0                 24
D71V5, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            2                 53
  CLUS_2            2                 21
  CLUS_3            4                 41
  CLUS_4            1                 24
D71V6, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            5                 50
  CLUS_3            3                 60
D71V7, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            3                 31
  CLUS_2            5                 63
  CLUS_3            1                 47
D71V8, multiclass
D71V9, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            3                 27
  CLUS_2            1                 48
  CLUS_3            5                 66
D71V10, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            3                 22
  CLUS_2            0                 36
  CLUS_3            6                 83

Clustering(72) Variable = 19q loss
D72V1, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            2                 43
  CLUS_2            0                 69
  CLUS_3            2                 34
D72V2, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            0                 37
  CLUS_2            2                 47
  CLUS_3            1                 39
  CLUS_4            1                 23
D72V3, multiclass
[1] "Remove cluster labels:" "19Q LOSS CNV"          
clus
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 1                 50 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LA         TCGA-BT-A2LB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C4-A0EZ         TCGA-C4-A0F0         TCGA-C4-A0F6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CF-A1HR         TCGA-CF-A1HS         TCGA-CF-A27C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2HX         TCGA-DK-A2I1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A2I2         TCGA-E5-A2PC         TCGA-FD-A3B3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FD-A3B4         TCGA-G2-A2EF         TCGA-G2-A2EJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G2-A2EK         TCGA-G2-A2EL         TCGA-G2-A2EO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G2-A2ES         TCGA-GD-A2C5         TCGA-H4-A2HO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-H4-A2HQ         TCGA-HQ-A2OE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D72V4, multiclass
[1] "Remove cluster labels:" "19Q LOSS CNV"          
clus
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 1                 50 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20P 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A20Q         TCGA-BT-A20R         TCGA-BT-A20T 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A20U         TCGA-BT-A20V         TCGA-BT-A20W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BT-A20X         TCGA-BT-A2LA         TCGA-BT-A2LB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C4-A0EZ         TCGA-C4-A0F0         TCGA-C4-A0F6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CF-A1HR         TCGA-CF-A1HS         TCGA-CF-A27C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A1A3         TCGA-DK-A1A5         TCGA-DK-A1A6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A1AA         TCGA-DK-A1AB         TCGA-DK-A1AC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A1AD         TCGA-DK-A1AE         TCGA-DK-A1AF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A1AG         TCGA-DK-A2HX         TCGA-DK-A2I1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DK-A2I2         TCGA-E5-A2PC         TCGA-FD-A3B3 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FD-A3B4         TCGA-G2-A2EF         TCGA-G2-A2EJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G2-A2EK         TCGA-G2-A2EL         TCGA-G2-A2EO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G2-A2ES         TCGA-GD-A2C5         TCGA-H4-A2HO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-H4-A2HQ         TCGA-HQ-A2OE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D72V5, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            2                 53
  CLUS_2            0                 23
  CLUS_3            2                 43
  CLUS_4            0                 25
D72V6, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            0                 30
  CLUS_2            2                 53
  CLUS_3            2                 61
D72V7, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            0                 34
  CLUS_2            4                 64
  CLUS_3            0                 48
D72V8, multiclass
D72V9, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            0                 30
  CLUS_2            0                 49
  CLUS_3            4                 67
D72V10, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            0                 25
  CLUS_2            0                 36
  CLUS_3            4                 85

Clustering(73) Variable = 20p loss
D73V1, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            4                 41
  CLUS_2            3                 66
  CLUS_3            0                 36
D73V2, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            3                 34
  CLUS_2            1                 48
  CLUS_3            0                 40
  CLUS_4            3                 21
D73V3, multiclass
[1] "Remove cluster labels:" "20P LOSS CNV"          
clus
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20Q 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A20R         TCGA-BT-A20T         TCGA-BT-A20U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A20V         TCGA-BT-A20W         TCGA-BT-A20X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A2LA         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DK-A1A5         TCGA-DK-A1A6         TCGA-DK-A1AA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DK-A1AB         TCGA-DK-A1AC         TCGA-DK-A1AD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HQ-A2OE 
"20P LOSS WILD-TYPE" 
D73V4, multiclass
[1] "Remove cluster labels:" "20P LOSS CNV"          
clus
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 2                 49 
        TCGA-BL-A0C8         TCGA-BL-A13I         TCGA-BL-A13J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A0S7         TCGA-BT-A0YX         TCGA-BT-A20J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A20N         TCGA-BT-A20O         TCGA-BT-A20Q 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A20R         TCGA-BT-A20T         TCGA-BT-A20U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A20V         TCGA-BT-A20W         TCGA-BT-A20X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BT-A2LA         TCGA-BT-A2LB         TCGA-C4-A0EZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C4-A0F0         TCGA-C4-A0F6         TCGA-CF-A1HR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CF-A1HS         TCGA-CF-A27C         TCGA-CU-A0YN 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DK-A1A5         TCGA-DK-A1A6         TCGA-DK-A1AA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DK-A1AB         TCGA-DK-A1AC         TCGA-DK-A1AD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DK-A1AE         TCGA-DK-A1AF         TCGA-DK-A1AG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DK-A2HX         TCGA-DK-A2I1         TCGA-DK-A2I2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-E5-A2PC         TCGA-FD-A3B3         TCGA-FD-A3B4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G2-A2EF         TCGA-G2-A2EJ         TCGA-G2-A2EK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G2-A2EL         TCGA-G2-A2EO         TCGA-G2-A2ES 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GD-A2C5         TCGA-H4-A2HO         TCGA-H4-A2HQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HQ-A2OE 
"20P LOSS WILD-TYPE" 
D73V5, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            4                 51
  CLUS_2            1                 22
  CLUS_3            1                 44
  CLUS_4            1                 24
D73V6, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                 29
  CLUS_2            5                 50
  CLUS_3            1                 62
D73V7, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            2                 32
  CLUS_2            3                 65
  CLUS_3            2                 46
D73V8, multiclass
D73V9, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            1                 48
  CLUS_3            4                 67
D73V10, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            2                 23
  CLUS_2            1                 35
  CLUS_3            4                 85

Clustering(74) Variable = 21q loss
D74V1, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            5                 40
  CLUS_2            6                 63
  CLUS_3            5                 31
D74V2, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            1                 36
  CLUS_2            8                 41
  CLUS_3            4                 36
  CLUS_4            3                 21
D74V3, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            2                  9
  CLUS_2            0                 10
  CLUS_3            1                 13
  CLUS_4            3                 13
D74V4, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            3                 10
  CLUS_2            2                 12
  CLUS_3            1                 23
D74V5, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            5                 50
  CLUS_2            1                 22
  CLUS_3            8                 37
  CLUS_4            2                 23
D74V6, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            4                 26
  CLUS_2            4                 51
  CLUS_3            8                 55
D74V7, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            3                 31
  CLUS_2            8                 60
  CLUS_3            5                 43
D74V8, multiclass
D74V9, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            2                 28
  CLUS_2            5                 44
  CLUS_3            9                 62
D74V10, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            2                 23
  CLUS_2            3                 33
  CLUS_3           11                 78

Clustering(75) Variable = 22q loss
D75V1, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           10                 35
  CLUS_2            6                 63
  CLUS_3           13                 23
D75V2, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            9                 28
  CLUS_2           10                 39
  CLUS_3            7                 33
  CLUS_4            3                 21
D75V3, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            4                  7
  CLUS_2            3                  7
  CLUS_3            0                 14
  CLUS_4            3                 13
D75V4, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            3                 10
  CLUS_2            5                  9
  CLUS_3            2                 22
D75V5, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            4                 51
  CLUS_2            8                 15
  CLUS_3           12                 33
  CLUS_4            3                 22
D75V6, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            4                 26
  CLUS_2            9                 46
  CLUS_3           14                 49
D75V7, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            5                 29
  CLUS_2           15                 53
  CLUS_3            9                 39
D75V8, multiclass
D75V9, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            3                 27
  CLUS_2           10                 39
  CLUS_3           16                 55
D75V10, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            4                 21
  CLUS_2            7                 29
  CLUS_3           18                 71

Clustering(76) Variable = Xq loss
D76V1, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           2                43
  CLUS_2           0                69
  CLUS_3           1                35
D76V2, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1                36
  CLUS_2           0                49
  CLUS_3           0                40
  CLUS_4           2                22
D76V3, multiclass
D76V4, multiclass
D76V5, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           2                53
  CLUS_2           1                22
  CLUS_3           0                45
  CLUS_4           0                25
D76V6, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                30
  CLUS_2           2                53
  CLUS_3           1                62
D76V7, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                34
  CLUS_2           1                67
  CLUS_3           2                46
D76V8, multiclass
D76V9, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                30
  CLUS_2           1                48
  CLUS_3           2                69
D76V10, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                25
  CLUS_2           0                36
  CLUS_3           3                86
                           V1                            V2 
                    "CN_CNMF"            "METHLYATION_CNMF" 
                           V3                            V4 
                  "RPPA_CNMF"          "RPPA_CHIERARCHICAL" 
                           V5                            V6 
               "MRNASEQ_CNMF"       "MRNASEQ_CHIERARCHICAL" 
                           V7                            V8 
                "MIRSEQ_CNMF"        "MIRSEQ_CHIERARCHICAL" 
                           V9                           V10 
         "MIRSEQ_MATURE_CNMF" "MIRSEQ_MATURE_CHIERARCHICAL" 
> q(save="no")
