
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/KIRP-TP/3142216/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/KIRP-TP/3144246/1.GDAC_mergedClustering.Finished/KIRP-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KIRP-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=KIRP-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=127, in cluster file=127, common to both=127
[1] "Reduce the number of clustering variables from 80 to 59."
[1]  59 127
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                9               118 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                9               118 
[1] "2p gain"
[1] 3
      2P GAIN CNV 2P GAIN WILD-TYPE 
               13               114 
      2P GAIN CNV 2P GAIN WILD-TYPE 
               13               114 
[1] "2q gain"
[1] 3
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               15               112 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               15               112 
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
               29                98 
      3P GAIN CNV 3P GAIN WILD-TYPE 
               29                98 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               33                94 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               33                94 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
                4               123 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                4               123 
[1] "4q gain"
[1] 3
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                3               124 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                3               124 
[1] "5p gain"
[1] 3
      5P GAIN CNV 5P GAIN WILD-TYPE 
               14               113 
      5P GAIN CNV 5P GAIN WILD-TYPE 
               14               113 
[1] "5q gain"
[1] 3
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               14               113 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               14               113 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
                4               123 
      6P GAIN CNV 6P GAIN WILD-TYPE 
                4               123 
[1] "6q gain"
[1] 3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                3               124 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                3               124 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
               67                60 
      7P GAIN CNV 7P GAIN WILD-TYPE 
               67                60 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               68                59 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               68                59 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
                9               118 
      8P GAIN CNV 8P GAIN WILD-TYPE 
                9               118 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               11               116 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               11               116 
[1] "10p gain"
[1] 3
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 4                123 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 4                123 
[1] "10q gain"
[1] 3
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 3                124 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 3                124 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                40                 87 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                40                 87 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                40                 87 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                40                 87 
[1] "13q gain"
[1] 3
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                14                113 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                14                113 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                60                 67 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                60                 67 
[1] "16q gain"
[1] 3
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                58                 69 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                58                 69 
[1] "17p gain"
[1] 3
      17P GAIN CNV 17P GAIN WILD-TYPE 
                66                 61 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                66                 61 
[1] "17q gain"
[1] 3
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                77                 50 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                77                 50 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 6                121 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 6                121 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 4                123 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 4                123 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                39                 88 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                39                 88 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                40                 87 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                40                 87 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 5                122 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 5                122 
[1] "Xq gain"
[1] 3
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                5               122 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                5               122 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
               14               113 
      1P LOSS CNV 1P LOSS WILD-TYPE 
               14               113 
[1] "1q loss"
[1] 3
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                7               120 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                7               120 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
                8               119 
      3P LOSS CNV 3P LOSS WILD-TYPE 
                8               119 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                3               124 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                3               124 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
               11               116 
      4P LOSS CNV 4P LOSS WILD-TYPE 
               11               116 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               12               115 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               12               115 
[1] "5p loss"
[1] 3
      5P LOSS CNV 5P LOSS WILD-TYPE 
                5               122 
      5P LOSS CNV 5P LOSS WILD-TYPE 
                5               122 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                6               121 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                6               121 
[1] "6p loss"
[1] 3
      6P LOSS CNV 6P LOSS WILD-TYPE 
                9               118 
      6P LOSS CNV 6P LOSS WILD-TYPE 
                9               118 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               12               115 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               12               115 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
                3               124 
      8P LOSS CNV 8P LOSS WILD-TYPE 
                3               124 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
               15               112 
      9P LOSS CNV 9P LOSS WILD-TYPE 
               15               112 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               17               110 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               17               110 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 7                120 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 7                120 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 8                119 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 8                119 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 9                118 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 9                118 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                11                116 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                11                116 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                12                115 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                12                115 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                23                104 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                23                104 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                11                116 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                11                116 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 3                124 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 3                124 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
                 5                122 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                 5                122 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                19                108 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                19                108 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                20                107 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                20                107 
[1] "19p loss"
[1] 3
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 4                123 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 4                123 
[1] "19q loss"
[1] 3
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 4                123 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 4                123 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                15                112 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                15                112 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                24                103 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                24                103 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                3               124 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                3               124 
[1] "data2feature, selection="
[1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
[4] "METHLYATION_CNMF"      "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 8 rows and 127 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MIRSEQ_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "MRNA_CNMF"             "MRNA_CHIERARCHICAL"    "CN_CNMF"              
[4] "METHLYATION_CNMF"      "MRNASEQ_CNMF"          "MRNASEQ_CHIERARCHICAL"
[7] "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 127 columns, 0 survival variables, and 8 non-survival variables.
MRNA_CNMF, nv=2, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=5, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1q gain
D1V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN CNV          1    0
  1Q GAIN WILD-TYPE    6    9
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           0                 9
D1V2, multiclass
[1] "Remove cluster labels:" "1Q GAIN CNV"           
clus
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                1                15 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
D1V3, multiclass
D1V4, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           1                26
  CLUS_2           0                53
  CLUS_3           7                24
D1V5, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           0                27
  CLUS_2           6                18
  CLUS_3           1                24
D1V6, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           3                15
  CLUS_2           0                37
  CLUS_3           4                17
D1V7, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           1                26
  CLUS_2           4                34
  CLUS_3           1                34
  CLUS_4           2                15
D1V8, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           3                24
  CLUS_2           5                40
  CLUS_3           0                12
  CLUS_4           0                33

Clustering(2) Variable = 2p gain
D2V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN CNV          2    1
  2P GAIN WILD-TYPE    5    8
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           2                 5
  CLUS_2           1                 8
D2V2, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           0                 4
  CLUS_2           2                 5
  CLUS_3           1                 4
D2V3, multiclass
D2V4, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           0                27
  CLUS_2           7                46
  CLUS_3           3                28
D2V5, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           5                22
  CLUS_2           3                21
  CLUS_3           2                23
D2V6, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           2                16
  CLUS_2           7                30
  CLUS_3           1                20
D2V7, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           2                25
  CLUS_2           3                35
  CLUS_3           4                31
  CLUS_4           2                15
D2V8, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           1                26
  CLUS_2           2                43
  CLUS_3           3                 9
  CLUS_4           5                28

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

Clustering(4) Variable = 3p gain
D4V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN CNV          4    2
  3P GAIN WILD-TYPE    3    7
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           4                 3
  CLUS_2           2                 7
D4V2, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0                 4
  CLUS_2           2                 5
  CLUS_3           4                 1
D4V3, multiclass
D4V4, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           4                23
  CLUS_2          17                36
  CLUS_3           2                29
D4V5, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1          12                15
  CLUS_2           0                24
  CLUS_3           7                18
D4V6, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0                18
  CLUS_2          19                18
  CLUS_3           0                21
D4V7, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           7                20
  CLUS_2           5                33
  CLUS_3          14                21
  CLUS_4           2                15
D4V8, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           1                26
  CLUS_2           6                39
  CLUS_3           8                 4
  CLUS_4          13                20

Clustering(5) Variable = 3q gain
D5V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN CNV          4    2
  3Q GAIN WILD-TYPE    3    7
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           4                 3
  CLUS_2           2                 7
D5V2, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           0                 4
  CLUS_2           2                 5
  CLUS_3           4                 1
D5V3, multiclass
D5V4, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           4                23
  CLUS_2          20                33
  CLUS_3           3                28
D5V5, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          14                13
  CLUS_2           0                24
  CLUS_3           8                17
D5V6, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           1                17
  CLUS_2          20                17
  CLUS_3           1                20
D5V7, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          10                17
  CLUS_2           5                33
  CLUS_3          15                20
  CLUS_4           2                15
D5V8, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           4                23
  CLUS_2           6                39
  CLUS_3           8                 4
  CLUS_4          14                19

Clustering(6) Variable = 4p gain
D6V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN CNV          2    0
  4P GAIN WILD-TYPE    5    9
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           2                 5
  CLUS_2           0                 9
D6V2, multiclass
[1] "Remove cluster labels:" "4P GAIN CNV"           
clus
      4P GAIN CNV 4P GAIN WILD-TYPE 
                2                14 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4115        TCGA-B9-4116 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D6V3, multiclass
D6V4, multiclass
[1] "Remove cluster labels:" "4P GAIN CNV"           
clus
      4P GAIN CNV 4P GAIN WILD-TYPE 
                2               109 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7584        TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-7915        TCGA-A4-7996        TCGA-A4-7997 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A48D        TCGA-AL-7173        TCGA-B1-5398 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B1-7332        TCGA-B1-A47M        TCGA-B1-A47N        TCGA-B1-A47O 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B3-8121        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-F9-A4JJ        TCGA-G7-6790 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7773 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GL-7966        TCGA-GL-8500        TCGA-GL-A4EM        TCGA-HE-7128 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HE-7129        TCGA-HE-7130        TCGA-IA-A40U        TCGA-IA-A40X 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-IZ-8195        TCGA-IZ-8196        TCGA-J7-6720 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-J7-8537 
"4P GAIN WILD-TYPE" 
D6V5, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           2                25
  CLUS_2           2                22
  CLUS_3           0                25
D6V6, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           1                17
  CLUS_2           2                35
  CLUS_3           1                20
D6V7, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           0                27
  CLUS_2           2                36
  CLUS_3           1                34
  CLUS_4           1                16
D6V8, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           1                26
  CLUS_2           1                44
  CLUS_3           0                12
  CLUS_4           2                31

Clustering(7) Variable = 4q gain
D7V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN CNV          1    0
  4Q GAIN WILD-TYPE    6    9
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           0                 9
D7V2, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4115 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D7V3, multiclass
D7V4, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                2               109 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7584        TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-7915        TCGA-A4-7996        TCGA-A4-7997 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A48D        TCGA-AL-7173        TCGA-B1-5398 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B1-7332        TCGA-B1-A47M        TCGA-B1-A47N        TCGA-B1-A47O 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B3-8121        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-F9-A4JJ        TCGA-G7-6790 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7773 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GL-7966        TCGA-GL-8500        TCGA-GL-A4EM        TCGA-HE-7128 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HE-7129        TCGA-HE-7130        TCGA-IA-A40U        TCGA-IA-A40X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-IZ-8195        TCGA-IZ-8196        TCGA-J7-6720 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-J7-8537 
"4Q GAIN WILD-TYPE" 
D7V5, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           2                25
  CLUS_2           1                23
  CLUS_3           0                25
D7V6, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           1                17
  CLUS_2           2                35
  CLUS_3           0                21
D7V7, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           0                27
  CLUS_2           1                37
  CLUS_3           1                34
  CLUS_4           1                16
D7V8, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           0                27
  CLUS_2           1                44
  CLUS_3           0                12
  CLUS_4           2                31

Clustering(8) Variable = 5p gain
D8V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV          2    0
  5P GAIN WILD-TYPE    5    9
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           2                 5
  CLUS_2           0                 9
D8V2, multiclass
[1] "Remove cluster labels:" "5P GAIN CNV"           
clus
      5P GAIN CNV 5P GAIN WILD-TYPE 
                2                14 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4617 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
D8V3, multiclass
D8V4, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           4                23
  CLUS_2           2                51
  CLUS_3           6                25
D8V5, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           2                25
  CLUS_2           5                19
  CLUS_3           1                24
D8V6, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           2                16
  CLUS_2           3                34
  CLUS_3           3                18
D8V7, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           2                25
  CLUS_2           3                35
  CLUS_3           3                32
  CLUS_4           3                14
D8V8, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           4                23
  CLUS_2           3                42
  CLUS_3           1                11
  CLUS_4           3                30

Clustering(9) Variable = 5q gain
D9V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN CNV          2    0
  5Q GAIN WILD-TYPE    5    9
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           2                 5
  CLUS_2           0                 9
D9V2, multiclass
[1] "Remove cluster labels:" "5Q GAIN CNV"           
clus
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                2                14 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4617 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D9V3, multiclass
D9V4, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           4                23
  CLUS_2           2                51
  CLUS_3           6                25
D9V5, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           2                25
  CLUS_2           4                20
  CLUS_3           2                23
D9V6, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           2                16
  CLUS_2           3                34
  CLUS_3           3                18
D9V7, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           3                24
  CLUS_2           3                35
  CLUS_3           3                32
  CLUS_4           2                15
D9V8, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           5                22
  CLUS_2           3                42
  CLUS_3           0                12
  CLUS_4           3                30

Clustering(10) Variable = 6p gain
D10V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV          1    0
  6P GAIN WILD-TYPE    6    9
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           0                 9
D10V2, multiclass
[1] "Remove cluster labels:" "6P GAIN CNV"           
clus
      6P GAIN CNV 6P GAIN WILD-TYPE 
                1                15 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D10V3, multiclass
D10V4, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           0                27
  CLUS_2           1                52
  CLUS_3           2                29
D10V5, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           1                26
  CLUS_2           3                21
  CLUS_3           0                25
D10V6, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           1                17
  CLUS_2           1                36
  CLUS_3           2                19
D10V7, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           0                27
  CLUS_2           3                35
  CLUS_3           0                35
  CLUS_4           1                16
D10V8, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           1                26
  CLUS_2           2                43
  CLUS_3           1                11
  CLUS_4           0                33

Clustering(11) Variable = 6q gain
D11V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV          1    0
  6Q GAIN WILD-TYPE    6    9
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           0                 9
D11V2, multiclass
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                1                15 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D11V3, multiclass
D11V4, multiclass
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                2               109 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7584        TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-7915        TCGA-A4-7996        TCGA-A4-7997 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A48D        TCGA-AL-7173        TCGA-B1-5398 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B1-7332        TCGA-B1-A47M        TCGA-B1-A47N        TCGA-B1-A47O 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B3-8121        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5894 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F9-A4JJ        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7773 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GL-7966        TCGA-GL-8500        TCGA-GL-A4EM        TCGA-HE-7128 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HE-7129        TCGA-HE-7130        TCGA-IA-A40U        TCGA-IA-A40X 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-IZ-8195        TCGA-IZ-8196        TCGA-J7-6720 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-J7-8537 
"6Q GAIN WILD-TYPE" 
D11V5, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1                26
  CLUS_2           2                22
  CLUS_3           0                25
D11V6, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1                17
  CLUS_2           1                36
  CLUS_3           1                20
D11V7, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           0                27
  CLUS_2           2                36
  CLUS_3           0                35
  CLUS_4           1                16
D11V8, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1                26
  CLUS_2           1                44
  CLUS_3           1                11
  CLUS_4           0                33

Clustering(12) Variable = 7p gain
D12V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN CNV          5    5
  7P GAIN WILD-TYPE    2    4
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           5                 2
  CLUS_2           5                 4
D12V2, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           3                 1
  CLUS_2           3                 4
  CLUS_3           4                 1
D12V3, multiclass
D12V4, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          10                17
  CLUS_2          40                13
  CLUS_3           7                24
D12V5, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          22                 5
  CLUS_2           5                19
  CLUS_3          12                13
D12V6, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           5                13
  CLUS_2          29                 8
  CLUS_3           5                16
D12V7, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          11                16
  CLUS_2          19                19
  CLUS_3          27                 8
  CLUS_4           7                10
D12V8, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          10                17
  CLUS_2          21                24
  CLUS_3          10                 2
  CLUS_4          23                10

Clustering(13) Variable = 7q gain
D13V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV          5    5
  7Q GAIN WILD-TYPE    2    4
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           5                 2
  CLUS_2           5                 4
D13V2, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           3                 1
  CLUS_2           3                 4
  CLUS_3           4                 1
D13V3, multiclass
D13V4, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          10                17
  CLUS_2          40                13
  CLUS_3           8                23
D13V5, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          22                 5
  CLUS_2           6                18
  CLUS_3          12                13
D13V6, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           6                12
  CLUS_2          29                 8
  CLUS_3           5                16
D13V7, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          11                16
  CLUS_2          19                19
  CLUS_3          28                 7
  CLUS_4           7                10
D13V8, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          10                17
  CLUS_2          22                23
  CLUS_3          10                 2
  CLUS_4          23                10

Clustering(14) Variable = 8p gain
D14V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV          0    1
  8P GAIN WILD-TYPE    7    8
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                 8
D14V2, multiclass
[1] "Remove cluster labels:" "8P GAIN CNV"           
clus
      8P GAIN CNV 8P GAIN WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3472 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D14V3, multiclass
D14V4, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           3                24
  CLUS_2           1                52
  CLUS_3           4                27
D14V5, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                26
  CLUS_2           2                22
  CLUS_3           2                23
D14V6, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                17
  CLUS_2           1                36
  CLUS_3           3                18
D14V7, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                26
  CLUS_2           4                34
  CLUS_3           2                33
  CLUS_4           0                17
D14V8, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                26
  CLUS_2           4                41
  CLUS_3           0                12
  CLUS_4           2                31

Clustering(15) Variable = 8q gain
D15V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV          1    1
  8Q GAIN WILD-TYPE    6    8
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           1                 8
D15V2, multiclass
[1] "Remove cluster labels:" "8Q GAIN CNV"           
clus
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                2                14 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3472        TCGA-AL-3473 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
D15V3, multiclass
D15V4, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           2                25
  CLUS_2           1                52
  CLUS_3           6                25
D15V5, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           1                26
  CLUS_2           4                20
  CLUS_3           2                23
D15V6, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           2                16
  CLUS_2           1                36
  CLUS_3           4                17
D15V7, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           1                26
  CLUS_2           6                32
  CLUS_3           2                33
  CLUS_4           0                17
D15V8, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           2                25
  CLUS_2           5                40
  CLUS_3           0                12
  CLUS_4           2                31

Clustering(16) Variable = 10p gain
D16V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN CNV          1    1
  10P GAIN WILD-TYPE    6    8
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            1                  8
D16V2, multiclass
[1] "Remove cluster labels:" "10P GAIN CNV"          
clus
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 2                 14 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3471 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B3-3925 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
D16V3, multiclass
D16V4, multiclass
[1] "Remove cluster labels:" "10P GAIN CNV"          
clus
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 2                109 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7584         TCGA-A4-7585 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7732         TCGA-A4-7734         TCGA-A4-7828 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-7996         TCGA-A4-7997 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8312 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-8630         TCGA-A4-A48D 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-5398         TCGA-B1-7332 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B1-A47M         TCGA-B1-A47N         TCGA-B1-A47O 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-5155         TCGA-B9-5156 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-BQ-5875 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DZ-6131 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-F9-A4JJ         TCGA-G7-6789 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-7966         TCGA-GL-8500 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-A4EM         TCGA-HE-7128         TCGA-HE-7129 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40X         TCGA-IA-A40Y 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IZ-8195         TCGA-IZ-8196         TCGA-J7-6720 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-J7-8537 
"10P GAIN WILD-TYPE" 
D16V5, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            2                 25
  CLUS_2            1                 23
  CLUS_3            0                 25
D16V6, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                 17
  CLUS_2            2                 35
  CLUS_3            0                 21
D16V7, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            0                 38
  CLUS_3            3                 32
  CLUS_4            0                 17
D16V8, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            1                 44
  CLUS_3            0                 12
  CLUS_4            2                 31

Clustering(17) Variable = 10q gain
D17V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN CNV          1    1
  10Q GAIN WILD-TYPE    6    8
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            1                  8
D17V2, multiclass
[1] "Remove cluster labels:" "10Q GAIN CNV"          
clus
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 2                 14 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3471 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B3-3925 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D17V3, multiclass
D17V4, multiclass
[1] "Remove cluster labels:" "10Q GAIN CNV"          
clus
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 1                110 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7584         TCGA-A4-7585 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7732         TCGA-A4-7734         TCGA-A4-7828 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-7996         TCGA-A4-7997 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8312 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-8630         TCGA-A4-A48D 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-5398         TCGA-B1-7332 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B1-A47M         TCGA-B1-A47N         TCGA-B1-A47O 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-5155         TCGA-B9-5156 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-BQ-5875 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DZ-6131 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-F9-A4JJ         TCGA-G7-6789 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-7966         TCGA-GL-8500 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-A4EM         TCGA-HE-7128         TCGA-HE-7129 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HE-7130         TCGA-IA-A40U         TCGA-IA-A40X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-J7-6720         TCGA-J7-8537 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D17V5, multiclass
[1] "Remove cluster labels:" "10Q GAIN CNV"          
clus
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 2                 74 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-5156         TCGA-BQ-5876 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7056 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DZ-6131         TCGA-DZ-6132 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-HE-7128 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HE-7129         TCGA-HE-7130 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D17V6, multiclass
[1] "Remove cluster labels:" "10Q GAIN CNV"          
clus
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 2                 74 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-5156         TCGA-BQ-5876 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7056 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DZ-6131         TCGA-DZ-6132 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-HE-7128 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HE-7129         TCGA-HE-7130 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D17V7, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            0                 38
  CLUS_3            2                 33
  CLUS_4            0                 17
D17V8, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            0                 45
  CLUS_3            0                 12
  CLUS_4            2                 31

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

Clustering(19) Variable = 12q gain
D19V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN CNV          3    3
  12Q GAIN WILD-TYPE    4    6
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            3                  4
  CLUS_2            3                  6
D19V2, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                  3
  CLUS_2            1                  6
  CLUS_3            4                  1
D19V3, multiclass
D19V4, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            9                 18
  CLUS_2           17                 36
  CLUS_3            8                 23
D19V5, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           12                 15
  CLUS_2            5                 19
  CLUS_3            6                 19
D19V6, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            3                 15
  CLUS_2           16                 21
  CLUS_3            4                 17
D19V7, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           12                 15
  CLUS_2            7                 31
  CLUS_3           12                 23
  CLUS_4            5                 12
D19V8, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           11                 16
  CLUS_2            8                 37
  CLUS_3            4                  8
  CLUS_4           13                 20

Clustering(20) Variable = 13q gain
D20V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN CNV          1    1
  13Q GAIN WILD-TYPE    6    8
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            1                  8
D20V2, multiclass
[1] "Remove cluster labels:" "13Q GAIN CNV"          
clus
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 2                 14 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B3-4104         TCGA-B9-4113         TCGA-B9-4114 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D20V3, multiclass
D20V4, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            5                 22
  CLUS_2            6                 47
  CLUS_3            1                 30
D20V5, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            5                 22
  CLUS_2            1                 23
  CLUS_3            4                 21
D20V6, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            2                 16
  CLUS_2            8                 29
  CLUS_3            0                 21
D20V7, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            3                 24
  CLUS_2            4                 34
  CLUS_3            6                 29
  CLUS_4            1                 16
D20V8, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            5                 40
  CLUS_3            4                  8
  CLUS_4            4                 29

Clustering(21) Variable = 16p gain
D21V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV          5    2
  16P GAIN WILD-TYPE    2    7
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            5                  2
  CLUS_2            2                  7
D21V2, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            0                  4
  CLUS_2            3                  4
  CLUS_3            4                  1
D21V3, multiclass
D21V4, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           11                 16
  CLUS_2           30                 23
  CLUS_3           12                 19
D21V5, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           15                 12
  CLUS_2            4                 20
  CLUS_3           13                 12
D21V6, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            2                 16
  CLUS_2           24                 13
  CLUS_3            6                 15
D21V7, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           14                 13
  CLUS_2           12                 26
  CLUS_3           24                 11
  CLUS_4            4                 13
D21V8, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           11                 16
  CLUS_2           12                 33
  CLUS_3            8                  4
  CLUS_4           23                 10

Clustering(22) Variable = 16q gain
D22V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN CNV          4    2
  16Q GAIN WILD-TYPE    3    7
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            4                  3
  CLUS_2            2                  7
D22V2, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            0                  4
  CLUS_2            2                  5
  CLUS_3            4                  1
D22V3, multiclass
D22V4, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           11                 16
  CLUS_2           31                 22
  CLUS_3           10                 21
D22V5, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           15                 12
  CLUS_2            3                 21
  CLUS_3           11                 14
D22V6, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            2                 16
  CLUS_2           24                 13
  CLUS_3            3                 18
D22V7, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           12                 15
  CLUS_2           11                 27
  CLUS_3           24                 11
  CLUS_4            4                 13
D22V8, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            8                 19
  CLUS_2           12                 33
  CLUS_3            8                  4
  CLUS_4           23                 10

Clustering(23) Variable = 17p gain
D23V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN CNV          5    5
  17P GAIN WILD-TYPE    2    4
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            5                  2
  CLUS_2            5                  4
D23V2, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            3                  1
  CLUS_2            3                  4
  CLUS_3            4                  1
D23V3, multiclass
D23V4, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            9                 18
  CLUS_2           40                 13
  CLUS_3            7                 24
D23V5, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1           20                  7
  CLUS_2            3                 21
  CLUS_3           10                 15
D23V6, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            3                 15
  CLUS_2           27                 10
  CLUS_3            3                 18
D23V7, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1           13                 14
  CLUS_2           17                 21
  CLUS_3           24                 11
  CLUS_4            7                 10
D23V8, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            8                 19
  CLUS_2           20                 25
  CLUS_3            9                  3
  CLUS_4           24                  9

Clustering(24) Variable = 17q gain
D24V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN CNV          6    5
  17Q GAIN WILD-TYPE    1    4
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            6                  1
  CLUS_2            5                  4
D24V2, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            3                  1
  CLUS_2            4                  3
  CLUS_3            4                  1
D24V3, multiclass
D24V4, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           11                 16
  CLUS_2           41                 12
  CLUS_3           14                 17
D24V5, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           20                  7
  CLUS_2            8                 16
  CLUS_3           13                 12
D24V6, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            6                 12
  CLUS_2           28                  9
  CLUS_3            7                 14
D24V7, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           16                 11
  CLUS_2           22                 16
  CLUS_3           25                 10
  CLUS_4            8                  9
D24V8, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           13                 14
  CLUS_2           25                 20
  CLUS_3            9                  3
  CLUS_4           24                  9

Clustering(25) Variable = 18p gain
D25V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          2    1
  18P GAIN WILD-TYPE    5    8
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            1                  8
D25V2, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            0                  4
  CLUS_2            3                  4
  CLUS_3            0                  5
D25V3, multiclass
D25V4, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            0                 27
  CLUS_2            3                 50
  CLUS_3            0                 31
D25V5, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                 25
  CLUS_2            2                 22
  CLUS_3            1                 24
D25V6, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            1                 17
  CLUS_2            3                 34
  CLUS_3            1                 20
D25V7, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            3                 35
  CLUS_3            2                 33
  CLUS_4            0                 17
D25V8, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            2                 43
  CLUS_3            1                 11
  CLUS_4            2                 31

Clustering(26) Variable = 18q gain
D26V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          1    0
  18Q GAIN WILD-TYPE    6    9
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            0                  9
D26V2, multiclass
[1] "Remove cluster labels:" "18Q GAIN CNV"          
clus
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 1                 15 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4104 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D26V3, multiclass
D26V4, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            0                 27
  CLUS_2            3                 50
  CLUS_3            0                 31
D26V5, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                 25
  CLUS_2            0                 24
  CLUS_3            1                 24
D26V6, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            0                 18
  CLUS_2            3                 34
  CLUS_3            0                 21
D26V7, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            1                 37
  CLUS_3            2                 33
  CLUS_4            0                 17
D26V8, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            0                 27
  CLUS_2            1                 44
  CLUS_3            1                 11
  CLUS_4            2                 31

Clustering(27) Variable = 20p gain
D27V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV          5    2
  20P GAIN WILD-TYPE    2    7
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            5                  2
  CLUS_2            2                  7
D27V2, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            0                  4
  CLUS_2            4                  3
  CLUS_3            3                  2
D27V3, multiclass
D27V4, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            5                 22
  CLUS_2           21                 32
  CLUS_3            6                 25
D27V5, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           15                 12
  CLUS_2            6                 18
  CLUS_3            2                 23
D27V6, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            3                 15
  CLUS_2           17                 20
  CLUS_3            3                 18
D27V7, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            8                 19
  CLUS_2           11                 27
  CLUS_3           15                 20
  CLUS_4            3                 14
D27V8, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            7                 20
  CLUS_2           10                 35
  CLUS_3            5                  7
  CLUS_4           15                 18

Clustering(28) Variable = 20q gain
D28V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV          5    3
  20Q GAIN WILD-TYPE    2    6
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            5                  2
  CLUS_2            3                  6
D28V2, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            0                  4
  CLUS_2            5                  2
  CLUS_3            3                  2
D28V3, multiclass
D28V4, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            5                 22
  CLUS_2           20                 33
  CLUS_3            7                 24
D28V5, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           15                 12
  CLUS_2            8                 16
  CLUS_3            2                 23
D28V6, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            5                 13
  CLUS_2           17                 20
  CLUS_3            3                 18
D28V7, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            7                 20
  CLUS_2           12                 26
  CLUS_3           16                 19
  CLUS_4            3                 14
D28V8, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            7                 20
  CLUS_2           12                 33
  CLUS_3            5                  7
  CLUS_4           14                 19

Clustering(29) Variable = 21q gain
D29V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN CNV          1    0
  21Q GAIN WILD-TYPE    6    9
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            0                  9
D29V2, multiclass
[1] "Remove cluster labels:" "21Q GAIN CNV"          
clus
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 1                 15 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B3-4104         TCGA-B9-4113         TCGA-B9-4114 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4617 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D29V3, multiclass
D29V4, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            3                 50
  CLUS_3            0                 31
D29V5, multiclass
[1] "Remove cluster labels:" "21Q GAIN CNV"          
clus
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 1                 75 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-B3-3925 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4617         TCGA-B9-5156 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-HE-7128         TCGA-HE-7129         TCGA-HE-7130 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D29V6, multiclass
[1] "Remove cluster labels:" "21Q GAIN CNV"          
clus
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 1                 75 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-B3-3925 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4617         TCGA-B9-5156 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-HE-7128         TCGA-HE-7129         TCGA-HE-7130 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D29V7, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            0                 27
  CLUS_2            0                 38
  CLUS_3            3                 32
  CLUS_4            1                 16
D29V8, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            0                 27
  CLUS_2            0                 45
  CLUS_3            1                 11
  CLUS_4            3                 30

Clustering(30) Variable = Xq gain
D30V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN CNV          0    1
  XQ GAIN WILD-TYPE    7    8
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                 8
D30V2, multiclass
[1] "Remove cluster labels:" "XQ GAIN CNV"           
clus
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-3926 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D30V3, multiclass
D30V4, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           0                27
  CLUS_2           1                52
  CLUS_3           3                28
D30V5, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           2                25
  CLUS_2           2                22
  CLUS_3           0                25
D30V6, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           1                17
  CLUS_2           2                35
  CLUS_3           1                20
D30V7, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           0                27
  CLUS_2           1                37
  CLUS_3           2                33
  CLUS_4           1                16
D30V8, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           1                26
  CLUS_2           1                44
  CLUS_3           0                12
  CLUS_4           2                31

Clustering(31) Variable = 1p loss
D31V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS CNV          0    1
  1P LOSS WILD-TYPE    7    8
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                 8
D31V2, multiclass
[1] "Remove cluster labels:" "1P LOSS CNV"           
clus
      1P LOSS CNV 1P LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D31V3, multiclass
D31V4, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           5                48
  CLUS_3           6                25
D31V5, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           3                24
  CLUS_2           1                23
  CLUS_3           1                24
D31V6, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           0                18
  CLUS_2           3                34
  CLUS_3           2                19
D31V7, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           4                23
  CLUS_2           0                38
  CLUS_3           7                28
  CLUS_4           1                16
D31V8, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           3                24
  CLUS_2           2                43
  CLUS_3           0                12
  CLUS_4           7                26

Clustering(32) Variable = 1q loss
D32V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS CNV          0    1
  1Q LOSS WILD-TYPE    7    8
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                 8
D32V2, multiclass
[1] "Remove cluster labels:" "1Q LOSS CNV"           
clus
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
D32V3, multiclass
D32V4, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           5                48
  CLUS_3           0                31
D32V5, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           3                24
  CLUS_2           0                24
  CLUS_3           0                25
D32V6, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                18
  CLUS_2           3                34
  CLUS_3           0                21
D32V7, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           0                38
  CLUS_3           5                30
  CLUS_4           0                17
D32V8, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                27
  CLUS_2           1                44
  CLUS_3           0                12
  CLUS_4           6                27

Clustering(33) Variable = 3p loss
D33V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          1    0
  3P LOSS WILD-TYPE    6    9
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           0                 9
D33V2, multiclass
[1] "Remove cluster labels:" "3P LOSS CNV"           
clus
      3P LOSS CNV 3P LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
D33V3, multiclass
D33V4, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           0                53
  CLUS_3           6                25
D33V5, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                27
  CLUS_2           4                20
  CLUS_3           2                23
D33V6, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           2                16
  CLUS_2           0                37
  CLUS_3           4                17
D33V7, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           2                36
  CLUS_3           0                35
  CLUS_4           3                14
D33V8, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           3                24
  CLUS_2           3                42
  CLUS_3           1                11
  CLUS_4           0                33

Clustering(34) Variable = 3q loss
D34V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS CNV          0    0
  3Q LOSS WILD-TYPE    7    9
D34V2, multiclass
D34V3, multiclass
D34V4, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           0                27
  CLUS_2           0                53
  CLUS_3           3                28
D34V5, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           0                27
  CLUS_2           3                21
  CLUS_3           0                25
D34V6, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           2                16
  CLUS_2           0                37
  CLUS_3           1                20
D34V7, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           1                37
  CLUS_3           0                35
  CLUS_4           1                16
D34V8, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           2                43
  CLUS_3           0                12
  CLUS_4           0                33

Clustering(35) Variable = 4p loss
D35V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV          0    1
  4P LOSS WILD-TYPE    7    8
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                 8
D35V2, multiclass
[1] "Remove cluster labels:" "4P LOSS CNV"           
clus
      4P LOSS CNV 4P LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D35V3, multiclass
D35V4, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           1                52
  CLUS_3           7                24
D35V5, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           5                19
  CLUS_3           0                25
D35V6, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           2                16
  CLUS_2           1                36
  CLUS_3           3                18
D35V7, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           4                34
  CLUS_3           1                34
  CLUS_4           2                15
D35V8, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           4                41
  CLUS_3           1                11
  CLUS_4           2                31

Clustering(36) Variable = 4q loss
D36V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV          0    1
  4Q LOSS WILD-TYPE    7    8
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                 8
D36V2, multiclass
[1] "Remove cluster labels:" "4Q LOSS CNV"           
clus
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
D36V3, multiclass
D36V4, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           1                52
  CLUS_3           8                23
D36V5, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           5                19
  CLUS_3           1                24
D36V6, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                16
  CLUS_2           1                36
  CLUS_3           4                17
D36V7, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           4                34
  CLUS_3           2                33
  CLUS_4           2                15
D36V8, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           4                41
  CLUS_3           2                10
  CLUS_4           2                31

Clustering(37) Variable = 5p loss
D37V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS CNV          0    0
  5P LOSS WILD-TYPE    7    9
D37V2, multiclass
D37V3, multiclass
D37V4, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           1                52
  CLUS_3           3                28
D37V5, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           3                21
  CLUS_3           0                25
D37V6, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           3                15
  CLUS_2           1                36
  CLUS_3           0                21
D37V7, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           3                35
  CLUS_3           0                35
  CLUS_4           0                17
D37V8, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           3                42
  CLUS_3           0                12
  CLUS_4           1                32

Clustering(38) Variable = 5q loss
D38V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS CNV          0    0
  5Q LOSS WILD-TYPE    7    9
D38V2, multiclass
D38V3, multiclass
D38V4, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           1                52
  CLUS_3           3                28
D38V5, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           2                22
  CLUS_3           0                25
D38V6, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           2                16
  CLUS_2           1                36
  CLUS_3           0                21
D38V7, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           3                35
  CLUS_3           0                35
  CLUS_4           0                17
D38V8, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           3                42
  CLUS_3           0                12
  CLUS_4           1                32

Clustering(39) Variable = 6p loss
D39V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS CNV          0    1
  6P LOSS WILD-TYPE    7    8
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                 8
D39V2, multiclass
[1] "Remove cluster labels:" "6P LOSS CNV"           
clus
      6P LOSS CNV 6P LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
D39V3, multiclass
D39V4, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           3                50
  CLUS_3           4                27
D39V5, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           4                23
  CLUS_2           3                21
  CLUS_3           1                24
D39V6, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           2                16
  CLUS_2           4                33
  CLUS_3           2                19
D39V7, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           2                36
  CLUS_3           5                30
  CLUS_4           0                17
D39V8, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           4                41
  CLUS_3           0                12
  CLUS_4           4                29

Clustering(40) Variable = 6q loss
D40V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          0    1
  6Q LOSS WILD-TYPE    7    8
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                 8
D40V2, multiclass
[1] "Remove cluster labels:" "6Q LOSS CNV"           
clus
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
D40V3, multiclass
D40V4, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           3                24
  CLUS_2           2                51
  CLUS_3           6                25
D40V5, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           3                24
  CLUS_2           4                20
  CLUS_3           1                24
D40V6, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           3                15
  CLUS_2           3                34
  CLUS_3           2                19
D40V7, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           3                35
  CLUS_3           5                30
  CLUS_4           1                16
D40V8, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           6                39
  CLUS_3           0                12
  CLUS_4           3                30

Clustering(41) Variable = 8p loss
D41V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV          0    1
  8P LOSS WILD-TYPE    7    8
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                 8
D41V2, multiclass
[1] "Remove cluster labels:" "8P LOSS CNV"           
clus
      8P LOSS CNV 8P LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
D41V3, multiclass
D41V4, multiclass
[1] "Remove cluster labels:" "8P LOSS CNV"           
clus
      8P LOSS CNV 8P LOSS WILD-TYPE 
                2               109 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7584        TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-7915        TCGA-A4-7996        TCGA-A4-7997 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A48D        TCGA-AL-7173        TCGA-B1-5398 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B1-A47M        TCGA-B1-A47N        TCGA-B1-A47O        TCGA-B3-8121 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268        TCGA-B9-A44B 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5561 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F9-A4JJ        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7773 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GL-7966        TCGA-GL-8500        TCGA-GL-A4EM        TCGA-HE-7128 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-HE-7129        TCGA-HE-7130        TCGA-IA-A40U        TCGA-IA-A40X 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-IZ-8195        TCGA-IZ-8196        TCGA-J7-6720 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-J7-8537 
"8P LOSS WILD-TYPE" 
D41V5, multiclass
[1] "Remove cluster labels:" "8P LOSS CNV"           
clus
      8P LOSS CNV 8P LOSS WILD-TYPE 
                2                74 
       TCGA-A4-7997        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B3-3925        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5156        TCGA-BQ-5876        TCGA-BQ-5877 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5561 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966        TCGA-HE-7128 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-HE-7129        TCGA-HE-7130 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
D41V6, multiclass
[1] "Remove cluster labels:" "8P LOSS CNV"           
clus
      8P LOSS CNV 8P LOSS WILD-TYPE 
                2                74 
       TCGA-A4-7997        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B3-3925        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5156        TCGA-BQ-5876        TCGA-BQ-5877 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5561 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966        TCGA-HE-7128 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-HE-7129        TCGA-HE-7130 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
D41V7, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           1                37
  CLUS_3           1                34
  CLUS_4           0                17
D41V8, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           0                27
  CLUS_2           1                44
  CLUS_3           0                12
  CLUS_4           2                31

Clustering(42) Variable = 9p loss
D42V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV          1    2
  9P LOSS WILD-TYPE    6    7
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           2                 7
D42V2, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           0                 4
  CLUS_2           2                 5
  CLUS_3           1                 4
D42V3, multiclass
D42V4, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           5                22
  CLUS_2           0                53
  CLUS_3           7                24
D42V5, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           8                16
  CLUS_3           2                23
D42V6, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           5                13
  CLUS_2           2                35
  CLUS_3           4                17
D42V7, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           7                31
  CLUS_3           3                32
  CLUS_4           3                14
D42V8, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           8                37
  CLUS_3           1                11
  CLUS_4           3                30

Clustering(43) Variable = 9q loss
D43V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS CNV          1    1
  9Q LOSS WILD-TYPE    6    8
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           1                 8
D43V2, multiclass
[1] "Remove cluster labels:" "9Q LOSS CNV"           
clus
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                2                14 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103        TCGA-B3-4104 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
D43V3, multiclass
D43V4, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           6                21
  CLUS_2           0                53
  CLUS_3           9                22
D43V5, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           7                17
  CLUS_3           2                23
D43V6, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           4                14
  CLUS_2           2                35
  CLUS_3           4                17
D43V7, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           1                26
  CLUS_2           7                31
  CLUS_3           4                31
  CLUS_4           2                15
D43V8, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           2                25
  CLUS_2           9                36
  CLUS_3           1                11
  CLUS_4           2                31

Clustering(44) Variable = 10p loss
D44V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          1    1
  10P LOSS WILD-TYPE    6    8
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            1                  8
D44V2, multiclass
[1] "Remove cluster labels:" "10P LOSS CNV"          
clus
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 2                 14 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B3-3925 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
D44V3, multiclass
D44V4, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            0                 27
  CLUS_2            1                 52
  CLUS_3            4                 27
D44V5, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            4                 20
  CLUS_3            1                 24
D44V6, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            2                 16
  CLUS_2            1                 36
  CLUS_3            3                 18
D44V7, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            0                 27
  CLUS_2            3                 35
  CLUS_3            1                 34
  CLUS_4            2                 15
D44V8, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            2                 25
  CLUS_2            2                 43
  CLUS_3            1                 11
  CLUS_4            1                 32

Clustering(45) Variable = 10q loss
D45V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          1    0
  10Q LOSS WILD-TYPE    6    9
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            0                  9
D45V2, multiclass
[1] "Remove cluster labels:" "10Q LOSS CNV"          
clus
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 1                 15 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B3-3925 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
D45V3, multiclass
D45V4, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            1                 52
  CLUS_3            5                 26
D45V5, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            4                 20
  CLUS_3            1                 24
D45V6, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                 17
  CLUS_2            1                 36
  CLUS_3            4                 17
D45V7, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            4                 34
  CLUS_3            1                 34
  CLUS_4            1                 16
D45V8, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            3                 24
  CLUS_2            3                 42
  CLUS_3            1                 11
  CLUS_4            0                 33

Clustering(46) Variable = 11p loss
D46V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV          0    1
  11P LOSS WILD-TYPE    7    8
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            1                  8
D46V2, multiclass
[1] "Remove cluster labels:" "11P LOSS CNV"          
clus
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 1                 15 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D46V3, multiclass
D46V4, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            2                 51
  CLUS_3            5                 26
D46V5, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            4                 20
  CLUS_3            1                 24
D46V6, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            3                 15
  CLUS_2            1                 36
  CLUS_3            2                 19
D46V7, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            2                 25
  CLUS_2            3                 35
  CLUS_3            2                 33
  CLUS_4            1                 16
D46V8, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            5                 40
  CLUS_3            1                 11
  CLUS_4            1                 32

Clustering(47) Variable = 11q loss
D47V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV          0    0
  11Q LOSS WILD-TYPE    7    9
D47V2, multiclass
D47V3, multiclass
D47V4, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            2                 51
  CLUS_3            8                 23
D47V5, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            4                 20
  CLUS_3            3                 22
D47V6, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            3                 15
  CLUS_2            1                 36
  CLUS_3            4                 17
D47V7, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            3                 24
  CLUS_2            3                 35
  CLUS_3            3                 32
  CLUS_4            1                 16
D47V8, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            2                 25
  CLUS_2            5                 40
  CLUS_3            1                 11
  CLUS_4            2                 31

Clustering(48) Variable = 13q loss
D48V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          0    1
  13Q LOSS WILD-TYPE    7    8
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            1                  8
D48V2, multiclass
[1] "Remove cluster labels:" "13Q LOSS CNV"          
clus
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 1                 15 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-4103         TCGA-B3-4104 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D48V3, multiclass
D48V4, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            2                 25
  CLUS_2            1                 52
  CLUS_3            8                 23
D48V5, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            2                 25
  CLUS_2            4                 20
  CLUS_3            0                 25
D48V6, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            3                 15
  CLUS_2            2                 35
  CLUS_3            1                 20
D48V7, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            6                 32
  CLUS_3            2                 33
  CLUS_4            1                 16
D48V8, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            2                 25
  CLUS_2            7                 38
  CLUS_3            0                 12
  CLUS_4            1                 32

Clustering(49) Variable = 14q loss
D49V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS CNV          2    2
  14Q LOSS WILD-TYPE    5    7
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            2                  7
D49V2, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            0                  4
  CLUS_2            3                  4
  CLUS_3            1                  4
D49V3, multiclass
D49V4, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            6                 21
  CLUS_2            6                 47
  CLUS_3            7                 24
D49V5, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            2                 25
  CLUS_2            7                 17
  CLUS_3            4                 21
D49V6, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            4                 14
  CLUS_2            3                 34
  CLUS_3            6                 15
D49V7, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            3                 24
  CLUS_2            7                 31
  CLUS_3            5                 30
  CLUS_4            5                 12
D49V8, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            5                 22
  CLUS_2            7                 38
  CLUS_3            2                 10
  CLUS_4            6                 27

Clustering(50) Variable = 15q loss
D50V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS CNV          0    1
  15Q LOSS WILD-TYPE    7    8
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            1                  8
D50V2, multiclass
[1] "Remove cluster labels:" "15Q LOSS CNV"          
clus
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 1                 15 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-4103         TCGA-B3-4104 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
D50V3, multiclass
D50V4, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            3                 24
  CLUS_2            2                 51
  CLUS_3            5                 26
D50V5, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            2                 25
  CLUS_2            4                 20
  CLUS_3            2                 23
D50V6, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            3                 15
  CLUS_2            4                 33
  CLUS_3            1                 20
D50V7, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            3                 24
  CLUS_2            3                 35
  CLUS_3            4                 31
  CLUS_4            0                 17
D50V8, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            2                 25
  CLUS_2            5                 40
  CLUS_3            0                 12
  CLUS_4            3                 30

Clustering(51) Variable = 16q loss
D51V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS CNV          0    0
  16Q LOSS WILD-TYPE    7    9
D51V2, multiclass
D51V3, multiclass
D51V4, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            0                 53
  CLUS_3            2                 29
D51V5, multiclass
[1] "Remove cluster labels:" "16Q LOSS CNV"          
clus
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 2                 74 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-B3-3925 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5876         TCGA-BQ-5877 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7056         TCGA-BQ-7058 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6795 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HE-7128         TCGA-HE-7129 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D51V6, multiclass
[1] "Remove cluster labels:" "16Q LOSS CNV"          
clus
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 2                 74 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-B3-3925 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5876         TCGA-BQ-5877 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7056         TCGA-BQ-7058 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6795 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HE-7128         TCGA-HE-7129 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D51V7, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            0                 27
  CLUS_2            2                 36
  CLUS_3            1                 34
  CLUS_4            0                 17
D51V8, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            0                 27
  CLUS_2            3                 42
  CLUS_3            0                 12
  CLUS_4            0                 33

Clustering(52) Variable = 17p loss
D52V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV          1    0
  17P LOSS WILD-TYPE    6    9
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            0                  9
D52V2, multiclass
[1] "Remove cluster labels:" "17P LOSS CNV"          
clus
      17P LOSS CNV 17P LOSS WILD-TYPE 
                 1                 15 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B3-3925 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
D52V3, multiclass
D52V4, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            0                 53
  CLUS_3            3                 28
D52V5, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            0                 27
  CLUS_2            3                 21
  CLUS_3            0                 25
D52V6, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            2                 16
  CLUS_2            0                 37
  CLUS_3            1                 20
D52V7, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            0                 27
  CLUS_2            4                 34
  CLUS_3            1                 34
  CLUS_4            0                 17
D52V8, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            4                 41
  CLUS_3            0                 12
  CLUS_4            0                 33

Clustering(53) Variable = 18p loss
D53V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV          0    1
  18P LOSS WILD-TYPE    7    8
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            1                  8
D53V2, multiclass
[1] "Remove cluster labels:" "18P LOSS CNV"          
clus
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 1                 15 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B3-4104         TCGA-B9-4113         TCGA-B9-4114 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4117         TCGA-B9-4617 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
D53V3, multiclass
D53V4, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            5                 22
  CLUS_2            4                 49
  CLUS_3            9                 22
D53V5, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            6                 18
  CLUS_3            3                 22
D53V6, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            5                 13
  CLUS_2            1                 36
  CLUS_3            4                 17
D53V7, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            7                 20
  CLUS_2            6                 32
  CLUS_3            2                 33
  CLUS_4            2                 15
D53V8, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            5                 22
  CLUS_2            8                 37
  CLUS_3            0                 12
  CLUS_4            4                 29

Clustering(54) Variable = 18q loss
D54V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV          0    1
  18Q LOSS WILD-TYPE    7    8
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            1                  8
D54V2, multiclass
[1] "Remove cluster labels:" "18Q LOSS CNV"          
clus
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 1                 15 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B3-4104         TCGA-B9-4113         TCGA-B9-4114 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4117         TCGA-B9-4617 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
D54V3, multiclass
D54V4, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            5                 22
  CLUS_2            4                 49
  CLUS_3           10                 21
D54V5, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            7                 17
  CLUS_3            3                 22
D54V6, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            6                 12
  CLUS_2            1                 36
  CLUS_3            4                 17
D54V7, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            7                 20
  CLUS_2            6                 32
  CLUS_3            3                 32
  CLUS_4            2                 15
D54V8, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            5                 22
  CLUS_2            9                 36
  CLUS_3            0                 12
  CLUS_4            4                 29

Clustering(55) Variable = 19p loss
D55V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS CNV          0    0
  19P LOSS WILD-TYPE    7    9
D55V2, multiclass
D55V3, multiclass
D55V4, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            2                 51
  CLUS_3            1                 30
D55V5, multiclass
[1] "Remove cluster labels:" "19P LOSS CNV"          
clus
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 2                 74 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-B3-3925 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5877         TCGA-BQ-5878 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-HE-7128 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-HE-7129         TCGA-HE-7130 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D55V6, multiclass
[1] "Remove cluster labels:" "19P LOSS CNV"          
clus
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 2                 74 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-B3-3925 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5877         TCGA-BQ-5878 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-HE-7128 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-HE-7129         TCGA-HE-7130 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D55V7, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            2                 25
  CLUS_2            1                 37
  CLUS_3            1                 34
  CLUS_4            0                 17
D55V8, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            0                 27
  CLUS_2            1                 44
  CLUS_3            1                 11
  CLUS_4            2                 31

Clustering(56) Variable = 19q loss
D56V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS CNV          0    0
  19Q LOSS WILD-TYPE    7    9
D56V2, multiclass
D56V3, multiclass
D56V4, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            2                 51
  CLUS_3            1                 30
D56V5, multiclass
[1] "Remove cluster labels:" "19Q LOSS CNV"          
clus
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 1                 75 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-B3-3925 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5876         TCGA-BQ-5877 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7056         TCGA-BQ-7058 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-GL-6846         TCGA-GL-7966 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HE-7128         TCGA-HE-7129         TCGA-HE-7130 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D56V6, multiclass
[1] "Remove cluster labels:" "19Q LOSS CNV"          
clus
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 1                 75 
        TCGA-A4-7997         TCGA-AL-3466         TCGA-AL-3467 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-B3-3925 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5876         TCGA-BQ-5877 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7056         TCGA-BQ-7058 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-GL-6846         TCGA-GL-7966 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HE-7128         TCGA-HE-7129         TCGA-HE-7130 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D56V7, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            2                 25
  CLUS_2            0                 38
  CLUS_3            1                 34
  CLUS_4            0                 17
D56V8, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            0                 27
  CLUS_2            1                 44
  CLUS_3            0                 12
  CLUS_4            2                 31

Clustering(57) Variable = 21q loss
D57V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV          2    1
  21Q LOSS WILD-TYPE    5    8
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            1                  8
D57V2, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            0                  4
  CLUS_2            1                  6
  CLUS_3            2                  3
D57V3, multiclass
D57V4, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            2                 25
  CLUS_2            4                 49
  CLUS_3            6                 25
D57V5, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            3                 24
  CLUS_2            1                 23
  CLUS_3            5                 20
D57V6, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            1                 17
  CLUS_2            5                 32
  CLUS_3            3                 18
D57V7, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            1                 26
  CLUS_2            3                 35
  CLUS_3            4                 31
  CLUS_4            4                 13
D57V8, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            5                 22
  CLUS_2            3                 42
  CLUS_3            0                 12
  CLUS_4            4                 29

Clustering(58) Variable = 22q loss
D58V1, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS CNV          1    1
  22Q LOSS WILD-TYPE    6    8
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            1                  8
D58V2, multiclass
[1] "Remove cluster labels:" "22Q LOSS CNV"          
clus
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                 2                 14 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B3-3925 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
D58V3, multiclass
D58V4, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            3                 24
  CLUS_2            6                 47
  CLUS_3           13                 18
D58V5, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            4                 23
  CLUS_2            6                 18
  CLUS_3            5                 20
D58V6, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            3                 15
  CLUS_2            4                 33
  CLUS_3            8                 13
D58V7, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            5                 22
  CLUS_2            4                 34
  CLUS_3            6                 29
  CLUS_4            6                 11
D58V8, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            6                 21
  CLUS_2            5                 40
  CLUS_3            2                 10
  CLUS_4            8                 25

Clustering(59) Variable = Xq loss
D59V1, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS CNV          0    1
  XQ LOSS WILD-TYPE    7    8
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                 8
D59V2, multiclass
[1] "Remove cluster labels:" "XQ LOSS CNV"           
clus
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                1                15 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B3-3925        TCGA-B3-4103 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B3-4104        TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4116        TCGA-B9-4117        TCGA-B9-4617 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D59V3, multiclass
D59V4, multiclass
[1] "Remove cluster labels:" "XQ LOSS CNV"           
clus
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                2               109 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7584        TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-7915        TCGA-A4-7996        TCGA-A4-7997 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A48D        TCGA-AL-7173        TCGA-B1-5398 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B1-7332        TCGA-B1-A47M        TCGA-B1-A47N        TCGA-B1-A47O 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B3-8121        TCGA-B9-5156        TCGA-B9-7268        TCGA-B9-A44B 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F9-A4JJ        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7773 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GL-7966        TCGA-GL-8500        TCGA-GL-A4EM        TCGA-HE-7128 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HE-7129        TCGA-HE-7130        TCGA-IA-A40U        TCGA-IA-A40X 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-IZ-8195        TCGA-IZ-8196        TCGA-J7-6720 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-J7-8537 
"XQ LOSS WILD-TYPE" 
D59V5, multiclass
[1] "Remove cluster labels:" "XQ LOSS CNV"           
clus
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                2                74 
       TCGA-A4-7997        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B3-3925        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5156        TCGA-BQ-5876        TCGA-BQ-5877 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966        TCGA-HE-7128 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HE-7129        TCGA-HE-7130 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D59V6, multiclass
[1] "Remove cluster labels:" "XQ LOSS CNV"           
clus
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                2                74 
       TCGA-A4-7997        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B3-3925        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5156        TCGA-BQ-5876        TCGA-BQ-5877 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966        TCGA-HE-7128 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HE-7129        TCGA-HE-7130 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D59V7, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                27
  CLUS_2           1                37
  CLUS_3           2                33
  CLUS_4           0                17
D59V8, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                27
  CLUS_2           0                45
  CLUS_3           1                11
  CLUS_4           2                31
                     V1                      V2                      V3 
            "MRNA_CNMF"    "MRNA_CHIERARCHICAL"               "CN_CNMF" 
                     V4                      V5                      V6 
     "METHLYATION_CNMF"          "MRNASEQ_CNMF" "MRNASEQ_CHIERARCHICAL" 
                     V7                      V8 
          "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
