
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/LIHC-TP/3142822/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/LIHC-TP/3144268/1.GDAC_mergedClustering.Finished/LIHC-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=LIHC-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=LIHC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=99, in cluster file=97, common to both=97
[1] "Reduce the number of clustering variables from 80 to 71."
[1] 71 97
[1] "1p gain"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
               10                87 
      1P GAIN CNV 1P GAIN WILD-TYPE 
               10                87 
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               51                46 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               51                46 
[1] "2p gain"
[1] 3
      2P GAIN CNV 2P GAIN WILD-TYPE 
                8                89 
      2P GAIN CNV 2P GAIN WILD-TYPE 
                8                89 
[1] "2q gain"
[1] 3
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
                7                90 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
                7                90 
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
                7                90 
      3P GAIN CNV 3P GAIN WILD-TYPE 
                7                90 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                7                90 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                7                90 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
                6                91 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                6                91 
[1] "5p gain"
[1] 3
      5P GAIN CNV 5P GAIN WILD-TYPE 
               28                69 
      5P GAIN CNV 5P GAIN WILD-TYPE 
               28                69 
[1] "5q gain"
[1] 3
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               20                77 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               20                77 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
               18                79 
      6P GAIN CNV 6P GAIN WILD-TYPE 
               18                79 
[1] "6q gain"
[1] 3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
               11                86 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
               11                86 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
               26                71 
      7P GAIN CNV 7P GAIN WILD-TYPE 
               26                71 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               26                71 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               26                71 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
               14                83 
      8P GAIN CNV 8P GAIN WILD-TYPE 
               14                83 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               45                52 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               45                52 
[1] "9p gain"
[1] 3
      9P GAIN CNV 9P GAIN WILD-TYPE 
                4                93 
      9P GAIN CNV 9P GAIN WILD-TYPE 
                4                93 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                3                94 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                3                94 
[1] "10p gain"
[1] 3
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 7                 90 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 7                 90 
[1] "10q gain"
[1] 3
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 4                 93 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 4                 93 
[1] "11q gain"
[1] 3
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 3                 94 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 3                 94 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 4                 93 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 4                 93 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 5                 92 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 5                 92 
[1] "13q gain"
[1] 3
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 5                 92 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 5                 92 
[1] "14q gain"
[1] 3
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 5                 92 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 5                 92 
[1] "15q gain"
[1] 3
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 5                 92 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 5                 92 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 4                 93 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 4                 93 
[1] "17p gain"
[1] 3
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 5                 92 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 5                 92 
[1] "17q gain"
[1] 3
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                20                 77 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                20                 77 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 3                 94 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 3                 94 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 4                 93 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 4                 93 
[1] "19p gain"
[1] 3
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 9                 88 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 9                 88 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                10                 87 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                10                 87 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                20                 77 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                20                 77 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                21                 76 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                21                 76 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 6                 91 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 6                 91 
[1] "22q gain"
[1] 3
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 8                 89 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 8                 89 
[1] "Xq gain"
[1] 3
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                5                92 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                5                92 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
               15                82 
      1P LOSS CNV 1P LOSS WILD-TYPE 
               15                82 
[1] "1q loss"
[1] 3
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                5                92 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                5                92 
[1] "2p loss"
[1] 3
      2P LOSS CNV 2P LOSS WILD-TYPE 
                3                94 
      2P LOSS CNV 2P LOSS WILD-TYPE 
                3                94 
[1] "2q loss"
[1] 3
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                4                93 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                4                93 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
                8                89 
      3P LOSS CNV 3P LOSS WILD-TYPE 
                8                89 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                3                94 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                3                94 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
                9                88 
      4P LOSS CNV 4P LOSS WILD-TYPE 
                9                88 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               18                79 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               18                79 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                5                92 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                5                92 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               20                77 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               20                77 
[1] "7p loss"
[1] 3
      7P LOSS CNV 7P LOSS WILD-TYPE 
                5                92 
      7P LOSS CNV 7P LOSS WILD-TYPE 
                5                92 
[1] "7q loss"
[1] 3
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                7                90 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                7                90 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
               41                56 
      8P LOSS CNV 8P LOSS WILD-TYPE 
               41                56 
[1] "8q loss"
[1] 3
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                6                91 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                6                91 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
               20                77 
      9P LOSS CNV 9P LOSS WILD-TYPE 
               20                77 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               19                78 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               19                78 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 6                 91 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 6                 91 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                17                 80 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                17                 80 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 6                 91 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 6                 91 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 8                 89 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 8                 89 
[1] "12p loss"
[1] 3
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 8                 89 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 8                 89 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                30                 67 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                30                 67 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                26                 71 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                26                 71 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 9                 88 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 9                 88 
[1] "16p loss"
[1] 3
      16P LOSS CNV 16P LOSS WILD-TYPE 
                20                 77 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                20                 77 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                27                 70 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                27                 70 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
                41                 56 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                41                 56 
[1] "17q loss"
[1] 3
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 6                 91 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 6                 91 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                10                 87 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                10                 87 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                11                 86 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                11                 86 
[1] "19p loss"
[1] 3
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 5                 92 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 5                 92 
[1] "20p loss"
[1] 3
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 5                 92 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 5                 92 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                16                 81 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                16                 81 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                10                 87 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                10                 87 
[1] "data2feature, selection="
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 

Input Data has 6 rows and 97 columns.

Variable 1:'CN_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'MRNASEQ_CNMF':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"               "METHLYATION_CNMF"      "MRNASEQ_CNMF"         
[4] "MRNASEQ_CHIERARCHICAL" "MIRSEQ_CNMF"           "MIRSEQ_CHIERARCHICAL" 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 97 columns, 0 survival variables, and 6 non-survival variables.
CN_CNMF, nv=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=9, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain
D1V1, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           4                24
  CLUS_2           4                32
  CLUS_3           2                31
D1V2, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           3                20
  CLUS_2           1                27
  CLUS_3           6                39
D1V3, multiclass
D1V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN CNV          4    5
  1P GAIN WILD-TYPE   25   35
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           4                25
  CLUS_2           5                35
D1V5, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           2                30
  CLUS_2           2                17
  CLUS_3           6                37
D1V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN CNV          2    8
  1P GAIN WILD-TYPE    9   75
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           2                 9
  CLUS_2           8                75

Clustering(2) Variable = 1q gain
D2V1, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          21                 7
  CLUS_2          12                24
  CLUS_3          18                15
D2V2, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           7                16
  CLUS_2          17                11
  CLUS_3          27                18
D2V3, multiclass
D2V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN CNV         16   18
  1Q GAIN WILD-TYPE   13   22
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          16                13
  CLUS_2          18                22
D2V5, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          15                17
  CLUS_2          10                 9
  CLUS_3          24                19
D2V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN CNV          6   43
  1Q GAIN WILD-TYPE    5   40
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           6                 5
  CLUS_2          43                40

Clustering(3) Variable = 2p gain
D3V1, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           1                27
  CLUS_2           4                32
  CLUS_3           3                30
D3V2, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           4                19
  CLUS_2           1                27
  CLUS_3           2                43
D3V3, multiclass
D3V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN CNV          4    3
  2P GAIN WILD-TYPE   25   37
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           4                25
  CLUS_2           3                37
D3V5, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           7                25
  CLUS_2           0                19
  CLUS_3           1                42
D3V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN CNV          0    8
  2P GAIN WILD-TYPE   11   75
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           0                11
  CLUS_2           8                75

Clustering(4) Variable = 2q gain
D4V1, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           1                27
  CLUS_2           4                32
  CLUS_3           2                31
D4V2, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           4                19
  CLUS_2           1                27
  CLUS_3           1                44
D4V3, multiclass
D4V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN CNV          4    2
  2Q GAIN WILD-TYPE   25   38
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           4                25
  CLUS_2           2                38
D4V5, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           6                26
  CLUS_2           0                19
  CLUS_3           1                42
D4V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN CNV          0    7
  2Q GAIN WILD-TYPE   11   76
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           0                11
  CLUS_2           7                76

Clustering(5) Variable = 3p gain
D5V1, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           3                25
  CLUS_2           1                35
  CLUS_3           3                30
D5V2, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           1                22
  CLUS_2           1                27
  CLUS_3           4                41
D5V3, multiclass
D5V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN CNV          3    3
  3P GAIN WILD-TYPE   26   37
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           3                26
  CLUS_2           3                37
D5V5, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           1                31
  CLUS_2           0                19
  CLUS_3           5                38
D5V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN CNV          0    6
  3P GAIN WILD-TYPE   11   77
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0                11
  CLUS_2           6                77

Clustering(6) Variable = 3q gain
D6V1, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           3                25
  CLUS_2           1                35
  CLUS_3           3                30
D6V2, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           1                22
  CLUS_2           1                27
  CLUS_3           4                41
D6V3, multiclass
D6V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN CNV          3    3
  3Q GAIN WILD-TYPE   26   37
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           3                26
  CLUS_2           3                37
D6V5, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           1                31
  CLUS_2           0                19
  CLUS_3           5                38
D6V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN CNV          0    6
  3Q GAIN WILD-TYPE   11   77
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           0                11
  CLUS_2           6                77

Clustering(7) Variable = 4p gain
D7V1, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           1                27
  CLUS_2           2                34
  CLUS_3           3                30
D7V2, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           1                22
  CLUS_2           4                24
  CLUS_3           1                44
D7V3, multiclass
D7V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN CNV          5    0
  4P GAIN WILD-TYPE   24   40
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           5                24
  CLUS_2           0                40
D7V5, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           4                28
  CLUS_2           0                19
  CLUS_3           2                41
D7V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN CNV          0    6
  4P GAIN WILD-TYPE   11   77
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           0                11
  CLUS_2           6                77

Clustering(8) Variable = 5p gain
D8V1, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          10                18
  CLUS_2           5                31
  CLUS_3          13                20
D8V2, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           4                19
  CLUS_2          11                17
  CLUS_3          13                32
D8V3, multiclass
D8V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV         10    7
  5P GAIN WILD-TYPE   19   33
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          10                19
  CLUS_2           7                33
D8V5, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           8                24
  CLUS_2           5                14
  CLUS_3          14                29
D8V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV          2   25
  5P GAIN WILD-TYPE    9   58
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           2                 9
  CLUS_2          25                58

Clustering(9) Variable = 5q gain
D9V1, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           9                19
  CLUS_2           4                32
  CLUS_3           7                26
D9V2, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           4                19
  CLUS_2           8                20
  CLUS_3           8                37
D9V3, multiclass
D9V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN CNV          7    5
  5Q GAIN WILD-TYPE   22   35
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           7                22
  CLUS_2           5                35
D9V5, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           5                27
  CLUS_2           2                17
  CLUS_3          12                31
D9V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN CNV          1   18
  5Q GAIN WILD-TYPE   10   65
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           1                10
  CLUS_2          18                65

Clustering(10) Variable = 6p gain
D10V1, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           8                20
  CLUS_2           1                35
  CLUS_3           9                24
D10V2, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           4                24
  CLUS_3          13                32
D10V3, multiclass
D10V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV          6   10
  6P GAIN WILD-TYPE   23   30
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           6                23
  CLUS_2          10                30
D10V5, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           3                29
  CLUS_2           4                15
  CLUS_3          10                33
D10V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV          2   15
  6P GAIN WILD-TYPE    9   68
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           2                 9
  CLUS_2          15                68

Clustering(11) Variable = 6q gain
D11V1, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           4                24
  CLUS_2           1                35
  CLUS_3           6                27
D11V2, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           3                25
  CLUS_3           8                37
D11V3, multiclass
D11V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV          5    5
  6Q GAIN WILD-TYPE   24   35
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           5                24
  CLUS_2           5                35
D11V5, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           2                30
  CLUS_2           3                16
  CLUS_3           6                37
D11V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV          1   10
  6Q GAIN WILD-TYPE   10   73
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1                10
  CLUS_2          10                73

Clustering(12) Variable = 7p gain
D12V1, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          12                16
  CLUS_2           9                27
  CLUS_3           5                28
D12V2, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           6                17
  CLUS_2           4                24
  CLUS_3          15                30
D12V3, multiclass
D12V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN CNV         11    8
  7P GAIN WILD-TYPE   18   32
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          11                18
  CLUS_2           8                32
D12V5, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           5                27
  CLUS_2           4                15
  CLUS_3          16                27
D12V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN CNV          3   22
  7P GAIN WILD-TYPE    8   61
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           3                 8
  CLUS_2          22                61

Clustering(13) Variable = 7q gain
D13V1, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          11                17
  CLUS_2          10                26
  CLUS_3           5                28
D13V2, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           6                17
  CLUS_2           2                26
  CLUS_3          17                28
D13V3, multiclass
D13V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV         11    9
  7Q GAIN WILD-TYPE   18   31
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          11                18
  CLUS_2           9                31
D13V5, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           6                26
  CLUS_2           4                15
  CLUS_3          15                28
D13V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV          3   22
  7Q GAIN WILD-TYPE    8   61
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           3                 8
  CLUS_2          22                61

Clustering(14) Variable = 8p gain
D14V1, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           6                22
  CLUS_2           3                33
  CLUS_3           5                28
D14V2, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           2                21
  CLUS_2           6                22
  CLUS_3           6                39
D14V3, multiclass
D14V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV          6    4
  8P GAIN WILD-TYPE   23   36
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           6                23
  CLUS_2           4                36
D14V5, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           5                27
  CLUS_2           1                18
  CLUS_3           7                36
D14V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV          1   12
  8P GAIN WILD-TYPE   10   71
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                10
  CLUS_2          12                71

Clustering(15) Variable = 8q gain
D15V1, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          26                 2
  CLUS_2           8                28
  CLUS_3          11                22
D15V2, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           9                14
  CLUS_2          14                14
  CLUS_3          21                24
D15V3, multiclass
D15V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV         15   18
  8Q GAIN WILD-TYPE   14   22
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          15                14
  CLUS_2          18                22
D15V5, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          13                19
  CLUS_2           6                13
  CLUS_3          24                19
D15V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV          3   40
  8Q GAIN WILD-TYPE    8   43
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           3                 8
  CLUS_2          40                43

Clustering(16) Variable = 9p gain
D16V1, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           0                28
  CLUS_2           1                35
  CLUS_3           3                30
D16V2, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           2                26
  CLUS_3           2                43
D16V3, multiclass
D16V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN CNV          2    1
  9P GAIN WILD-TYPE   27   39
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2                27
  CLUS_2           1                39
D16V5, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           0                32
  CLUS_2           0                19
  CLUS_3           4                39
D16V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN CNV          0    4
  9P GAIN WILD-TYPE   11   79
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           0                11
  CLUS_2           4                79

Clustering(17) Variable = 9q gain
D17V1, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                28
  CLUS_2           1                35
  CLUS_3           2                31
D17V2, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           1                27
  CLUS_3           2                43
D17V3, multiclass
D17V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN CNV          2    1
  9Q GAIN WILD-TYPE   27   39
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                27
  CLUS_2           1                39
D17V5, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                32
  CLUS_2           0                19
  CLUS_3           3                40
D17V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN CNV          0    3
  9Q GAIN WILD-TYPE   11   80
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                11
  CLUS_2           3                80

Clustering(18) Variable = 10p gain
D18V1, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            2                 34
  CLUS_3            4                 29
D18V2, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            3                 25
  CLUS_3            2                 43
D18V3, multiclass
D18V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN CNV          6    1
  10P GAIN WILD-TYPE   23   39
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            6                 23
  CLUS_2            1                 39
D18V5, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            3                 29
  CLUS_2            0                 19
  CLUS_3            4                 39
D18V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN CNV          0    7
  10P GAIN WILD-TYPE   11   76
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            7                 76

Clustering(19) Variable = 10q gain
D19V1, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            2                 26
  CLUS_2            0                 36
  CLUS_3            2                 31
D19V2, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            2                 26
  CLUS_3            1                 44
D19V3, multiclass
D19V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN CNV          2    1
  10Q GAIN WILD-TYPE   27   39
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            2                 27
  CLUS_2            1                 39
D19V5, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            0                 32
  CLUS_2            0                 19
  CLUS_3            4                 39
D19V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN CNV          0    4
  10Q GAIN WILD-TYPE   11   79
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            4                 79

Clustering(20) Variable = 11q gain
D20V1, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            2                 26
  CLUS_2            0                 36
  CLUS_3            1                 32
D20V2, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            0                 28
  CLUS_3            3                 42
D20V3, multiclass
[1] "Remove cluster labels:" "11Q GAIN CNV"          
clus
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 1                 68 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A112 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A216         TCGA-BC-A217         TCGA-BC-A3KF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BC-A3KG         TCGA-BD-A2L6         TCGA-CC-5258 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5262         TCGA-CC-5263 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CC-5264         TCGA-CC-A1HT         TCGA-CC-A3MB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A11B         TCGA-DD-A11C         TCGA-DD-A11D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EG         TCGA-DD-A1EH         TCGA-DD-A1EI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A1EJ         TCGA-DD-A1EL         TCGA-DD-A39X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DD-A3A2         TCGA-EP-A12J         TCGA-EP-A26S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A2QQ         TCGA-FV-A3I1         TCGA-FV-A3R2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FV-A3R3         TCGA-G3-A25S         TCGA-G3-A25T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D20V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN CNV          1    0
  11Q GAIN WILD-TYPE   28   40
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            1                 28
  CLUS_2            0                 40
D20V5, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            1                 31
  CLUS_2            1                 18
  CLUS_3            1                 42
D20V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN CNV          0    3
  11Q GAIN WILD-TYPE   11   80
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            3                 80

Clustering(21) Variable = 12p gain
D21V1, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            1                 35
  CLUS_3            3                 30
D21V2, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            2                 26
  CLUS_3            1                 44
D21V3, multiclass
[1] "Remove cluster labels:" "12P GAIN CNV"          
clus
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 2                 67 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A112 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A216         TCGA-BC-A217         TCGA-BC-A3KF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BC-A3KG         TCGA-BD-A2L6         TCGA-CC-5258 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5262         TCGA-CC-5263 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CC-A1HT         TCGA-CC-A3MB         TCGA-DD-A113 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A114         TCGA-DD-A115         TCGA-DD-A116 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A118         TCGA-DD-A119         TCGA-DD-A11B 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1EA 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39X         TCGA-DD-A39Y 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DD-A3A2         TCGA-EP-A12J         TCGA-EP-A26S 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A23B 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A2QQ         TCGA-FV-A3I1         TCGA-FV-A3R2 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FV-A3R3         TCGA-G3-A25S         TCGA-G3-A25U 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25X         TCGA-G3-A25Y 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CH         TCGA-G3-A3CJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G3-A3CK 
"12P GAIN WILD-TYPE" 
D21V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN CNV          2    0
  12P GAIN WILD-TYPE   27   40
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            2                 27
  CLUS_2            0                 40
D21V5, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            2                 30
  CLUS_2            0                 19
  CLUS_3            2                 41
D21V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN CNV          0    4
  12P GAIN WILD-TYPE   11   79
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            4                 79

Clustering(22) Variable = 12q gain
D22V1, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            1                 35
  CLUS_3            4                 29
D22V2, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            2                 26
  CLUS_3            2                 43
D22V3, multiclass
D22V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN CNV          2    1
  12Q GAIN WILD-TYPE   27   39
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            2                 27
  CLUS_2            1                 39
D22V5, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            2                 30
  CLUS_2            0                 19
  CLUS_3            3                 40
D22V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN CNV          0    5
  12Q GAIN WILD-TYPE   11   78
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            5                 78

Clustering(23) Variable = 13q gain
D23V1, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            0                 36
  CLUS_3            4                 29
D23V2, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            2                 26
  CLUS_3            3                 42
D23V3, multiclass
D23V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN CNV          3    1
  13Q GAIN WILD-TYPE   26   39
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            3                 26
  CLUS_2            1                 39
D23V5, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            0                 32
  CLUS_2            1                 18
  CLUS_3            4                 39
D23V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN CNV          0    5
  13Q GAIN WILD-TYPE   11   78
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            5                 78

Clustering(24) Variable = 14q gain
D24V1, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            3                 33
  CLUS_3            2                 31
D24V2, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            2                 21
  CLUS_2            1                 27
  CLUS_3            1                 44
D24V3, multiclass
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 2                 67 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A112 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A216         TCGA-BC-A217         TCGA-BC-A3KF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BC-A3KG         TCGA-CC-5258         TCGA-CC-5260 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-5264 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CC-A1HT         TCGA-CC-A3MB         TCGA-DD-A113 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A114         TCGA-DD-A115         TCGA-DD-A116 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A118         TCGA-DD-A119         TCGA-DD-A11B 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1EA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EF         TCGA-DD-A1EG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-DD-A39X         TCGA-DD-A39Y 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DD-A3A2         TCGA-EP-A12J         TCGA-EP-A26S 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FV-A3I1         TCGA-FV-A3R2         TCGA-FV-A3R3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25X         TCGA-G3-A25Y 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CH         TCGA-G3-A3CJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK 
"14Q GAIN WILD-TYPE" 
D24V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN CNV          0    2
  14Q GAIN WILD-TYPE   29   38
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            0                 29
  CLUS_2            2                 38
D24V5, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            2                 30
  CLUS_2            1                 18
  CLUS_3            2                 41
D24V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN CNV          1    4
  14Q GAIN WILD-TYPE   10   79
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            1                 10
  CLUS_2            4                 79

Clustering(25) Variable = 15q gain
D25V1, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            2                 34
  CLUS_3            3                 30
D25V2, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            2                 21
  CLUS_2            0                 28
  CLUS_3            2                 43
D25V3, multiclass
D25V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN CNV          2    3
  15Q GAIN WILD-TYPE   27   37
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            2                 27
  CLUS_2            3                 37
D25V5, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            2                 30
  CLUS_2            1                 18
  CLUS_3            2                 41
D25V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN CNV          0    5
  15Q GAIN WILD-TYPE   11   78
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            5                 78

Clustering(26) Variable = 16p gain
D26V1, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            1                 35
  CLUS_3            3                 30
D26V2, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            2                 26
  CLUS_3            2                 43
D26V3, multiclass
[1] "Remove cluster labels:" "16P GAIN CNV"          
clus
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 2                 67 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10S         TCGA-BC-A10T         TCGA-BC-A10U 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10W         TCGA-BC-A10X         TCGA-BC-A10Y 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10Z         TCGA-BC-A216         TCGA-BC-A217 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-BD-A2L6 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5258         TCGA-CC-5260         TCGA-CC-5262 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-5264         TCGA-CC-A1HT 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-A3MB         TCGA-DD-A113         TCGA-DD-A114 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11B         TCGA-DD-A11C 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1EA         TCGA-DD-A1EB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1ED         TCGA-DD-A1EE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EF         TCGA-DD-A1EG         TCGA-DD-A1EH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A3A2 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-ES-A2HS 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QQ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A3I1         TCGA-FV-A3R2         TCGA-FV-A3R3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25X         TCGA-G3-A25Y 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CH         TCGA-G3-A3CJ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CK 
"16P GAIN WILD-TYPE" 
D26V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV          2    0
  16P GAIN WILD-TYPE   27   40
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            2                 27
  CLUS_2            0                 40
D26V5, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            2                 30
  CLUS_2            1                 18
  CLUS_3            1                 42
D26V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV          0    4
  16P GAIN WILD-TYPE   11   79
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            4                 79

Clustering(27) Variable = 17p gain
D27V1, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            2                 34
  CLUS_3            3                 30
D27V2, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            2                 21
  CLUS_2            2                 26
  CLUS_3            0                 45
D27V3, multiclass
D27V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN CNV          2    1
  17P GAIN WILD-TYPE   27   39
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            2                 27
  CLUS_2            1                 39
D27V5, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            2                 30
  CLUS_2            0                 19
  CLUS_3            3                 40
D27V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN CNV          0    5
  17P GAIN WILD-TYPE   11   78
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            5                 78

Clustering(28) Variable = 17q gain
D28V1, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            2                 26
  CLUS_2            7                 29
  CLUS_3           11                 22
D28V2, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            5                 18
  CLUS_2            5                 23
  CLUS_3            9                 36
D28V3, multiclass
D28V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN CNV          8    8
  17Q GAIN WILD-TYPE   21   32
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            8                 21
  CLUS_2            8                 32
D28V5, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            8                 24
  CLUS_2            3                 16
  CLUS_3            9                 34
D28V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN CNV          1   19
  17Q GAIN WILD-TYPE   10   64
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            1                 10
  CLUS_2           19                 64

Clustering(29) Variable = 18p gain
D29V1, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                 26
  CLUS_2            0                 36
  CLUS_3            1                 32
D29V2, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            2                 26
  CLUS_3            1                 44
D29V3, multiclass
[1] "Remove cluster labels:" "18P GAIN CNV"          
clus
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 2                 67 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A112 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A216         TCGA-BC-A217         TCGA-BC-A3KF 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A3KG         TCGA-BD-A2L6         TCGA-CC-5258 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5262         TCGA-CC-5264 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-A1HT         TCGA-CC-A3MB         TCGA-DD-A114 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11B         TCGA-DD-A11C 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1EA         TCGA-DD-A1EB 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1ED         TCGA-DD-A1EE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EF         TCGA-DD-A1EG         TCGA-DD-A1EH 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A3A2 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-ES-A2HS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A3I1         TCGA-FV-A3R2         TCGA-FV-A3R3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25X         TCGA-G3-A25Y 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CH         TCGA-G3-A3CJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A3CK 
"18P GAIN WILD-TYPE" 
D29V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          2    0
  18P GAIN WILD-TYPE   27   40
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                 27
  CLUS_2            0                 40
D29V5, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            1                 31
  CLUS_2            1                 18
  CLUS_3            1                 42
D29V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          0    3
  18P GAIN WILD-TYPE   11   80
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            3                 80

Clustering(30) Variable = 18q gain
D30V1, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                 26
  CLUS_2            0                 36
  CLUS_3            2                 31
D30V2, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            3                 25
  CLUS_3            1                 44
D30V3, multiclass
D30V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          3    0
  18Q GAIN WILD-TYPE   26   40
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            3                 26
  CLUS_2            0                 40
D30V5, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                 30
  CLUS_2            1                 18
  CLUS_3            1                 42
D30V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          0    4
  18Q GAIN WILD-TYPE   11   79
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            4                 79

Clustering(31) Variable = 19p gain
D31V1, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            4                 24
  CLUS_2            1                 35
  CLUS_3            4                 29
D31V2, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            6                 22
  CLUS_3            1                 44
D31V3, multiclass
D31V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN CNV          6    1
  19P GAIN WILD-TYPE   23   39
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            6                 23
  CLUS_2            1                 39
D31V5, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            0                 32
  CLUS_2            0                 19
  CLUS_3            9                 34
D31V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN CNV          0    9
  19P GAIN WILD-TYPE   11   74
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            9                 74

Clustering(32) Variable = 19q gain
D32V1, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            4                 24
  CLUS_2            2                 34
  CLUS_3            4                 29
D32V2, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            7                 21
  CLUS_3            1                 44
D32V3, multiclass
D32V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN CNV          8    1
  19Q GAIN WILD-TYPE   21   39
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            8                 21
  CLUS_2            1                 39
D32V5, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            2                 30
  CLUS_2            0                 19
  CLUS_3            8                 35
D32V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN CNV          0   10
  19Q GAIN WILD-TYPE   11   73
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2           10                 73

Clustering(33) Variable = 20p gain
D33V1, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            6                 22
  CLUS_2            5                 31
  CLUS_3            9                 24
D33V2, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            3                 20
  CLUS_2            8                 20
  CLUS_3            8                 37
D33V3, multiclass
D33V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV          9    6
  20P GAIN WILD-TYPE   20   34
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            9                 20
  CLUS_2            6                 34
D33V5, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            6                 26
  CLUS_2            2                 17
  CLUS_3           11                 32
D33V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV          2   17
  20P GAIN WILD-TYPE    9   66
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            2                  9
  CLUS_2           17                 66

Clustering(34) Variable = 20q gain
D34V1, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            6                 22
  CLUS_2            5                 31
  CLUS_3           10                 23
D34V2, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            3                 20
  CLUS_2            8                 20
  CLUS_3            9                 36
D34V3, multiclass
D34V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV          9    7
  20Q GAIN WILD-TYPE   20   33
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            9                 20
  CLUS_2            7                 33
D34V5, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            6                 26
  CLUS_2            2                 17
  CLUS_3           12                 31
D34V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV          2   18
  20Q GAIN WILD-TYPE    9   65
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            2                  9
  CLUS_2           18                 65

Clustering(35) Variable = 21q gain
D35V1, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            1                 35
  CLUS_3            4                 29
D35V2, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            3                 25
  CLUS_3            1                 44
D35V3, multiclass
D35V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN CNV          3    1
  21Q GAIN WILD-TYPE   26   39
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            3                 26
  CLUS_2            1                 39
D35V5, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            2                 30
  CLUS_2            1                 18
  CLUS_3            3                 40
D35V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN CNV          0    6
  21Q GAIN WILD-TYPE   11   77
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            6                 77

Clustering(36) Variable = 22q gain
D36V1, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            2                 34
  CLUS_3            5                 28
D36V2, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            3                 25
  CLUS_3            4                 41
D36V3, multiclass
D36V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN CNV          5    2
  22Q GAIN WILD-TYPE   24   38
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            5                 24
  CLUS_2            2                 38
D36V5, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            3                 29
  CLUS_2            1                 18
  CLUS_3            4                 39
D36V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN CNV          0    8
  22Q GAIN WILD-TYPE   11   75
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            0                 11
  CLUS_2            8                 75

Clustering(37) Variable = Xq gain
D37V1, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           3                25
  CLUS_2           0                36
  CLUS_3           2                31
D37V2, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           0                28
  CLUS_3           5                40
D37V3, multiclass
D37V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN CNV          0    3
  XQ GAIN WILD-TYPE   29   37
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           0                29
  CLUS_2           3                37
D37V5, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           0                32
  CLUS_2           1                18
  CLUS_3           4                39
D37V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN CNV          1    4
  XQ GAIN WILD-TYPE   10   79
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           1                10
  CLUS_2           4                79

Clustering(38) Variable = 1p loss
D38V1, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           4                24
  CLUS_2           4                32
  CLUS_3           7                26
D38V2, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           0                23
  CLUS_2           6                22
  CLUS_3           8                37
D38V3, multiclass
D38V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS CNV          6    8
  1P LOSS WILD-TYPE   23   32
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           6                23
  CLUS_2           8                32
D38V5, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           3                29
  CLUS_2           2                17
  CLUS_3          10                33
D38V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS CNV          1   14
  1P LOSS WILD-TYPE   10   69
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1                10
  CLUS_2          14                69

Clustering(39) Variable = 1q loss
D39V1, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                28
  CLUS_2           2                34
  CLUS_3           3                30
D39V2, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                23
  CLUS_2           0                28
  CLUS_3           4                41
D39V3, multiclass
D39V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS CNV          2    3
  1Q LOSS WILD-TYPE   27   37
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2                27
  CLUS_2           3                37
D39V5, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           1                31
  CLUS_2           0                19
  CLUS_3           4                39
D39V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS CNV          0    5
  1Q LOSS WILD-TYPE   11   78
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                11
  CLUS_2           5                78

Clustering(40) Variable = 2p loss
D40V1, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1                27
  CLUS_2           0                36
  CLUS_3           2                31
D40V2, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1                22
  CLUS_2           0                28
  CLUS_3           2                43
D40V3, multiclass
D40V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS CNV          0    3
  2P LOSS WILD-TYPE   29   37
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                29
  CLUS_2           3                37
D40V5, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                32
  CLUS_2           1                18
  CLUS_3           2                41
D40V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS CNV          0    3
  2P LOSS WILD-TYPE   11   80
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                11
  CLUS_2           3                80

Clustering(41) Variable = 2q loss
D41V1, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1                27
  CLUS_2           0                36
  CLUS_3           3                30
D41V2, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1                22
  CLUS_2           0                28
  CLUS_3           3                42
D41V3, multiclass
D41V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS CNV          1    3
  2Q LOSS WILD-TYPE   28   37
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1                28
  CLUS_2           3                37
D41V5, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0                32
  CLUS_2           1                18
  CLUS_3           3                40
D41V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS CNV          0    4
  2Q LOSS WILD-TYPE   11   79
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0                11
  CLUS_2           4                79

Clustering(42) Variable = 3p loss
D42V1, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           2                26
  CLUS_2           1                35
  CLUS_3           5                28
D42V2, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           1                22
  CLUS_2           5                23
  CLUS_3           2                43
D42V3, multiclass
D42V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          6    0
  3P LOSS WILD-TYPE   23   40
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           6                23
  CLUS_2           0                40
D42V5, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           5                27
  CLUS_2           1                18
  CLUS_3           2                41
D42V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          0    8
  3P LOSS WILD-TYPE   11   75
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                11
  CLUS_2           8                75

Clustering(43) Variable = 3q loss
D43V1, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           2                26
  CLUS_2           0                36
  CLUS_3           1                32
D43V2, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           0                23
  CLUS_2           3                25
  CLUS_3           0                45
D43V3, multiclass
D43V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS CNV          3    0
  3Q LOSS WILD-TYPE   26   40
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           3                26
  CLUS_2           0                40
D43V5, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           1                31
  CLUS_2           0                19
  CLUS_3           2                41
D43V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS CNV          0    3
  3Q LOSS WILD-TYPE   11   80
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           0                11
  CLUS_2           3                80

Clustering(44) Variable = 4p loss
D44V1, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           1                27
  CLUS_2           1                35
  CLUS_3           7                26
D44V2, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           1                22
  CLUS_2           4                24
  CLUS_3           4                41
D44V3, multiclass
D44V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV          5    4
  4P LOSS WILD-TYPE   24   36
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           5                24
  CLUS_2           4                36
D44V5, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           3                29
  CLUS_2           3                16
  CLUS_3           3                40
D44V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV          2    7
  4P LOSS WILD-TYPE    9   76
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           2                 9
  CLUS_2           7                76

Clustering(45) Variable = 4q loss
D45V1, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           5                23
  CLUS_2           1                35
  CLUS_3          12                21
D45V2, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           3                20
  CLUS_2           7                21
  CLUS_3           8                37
D45V3, multiclass
D45V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV          7    9
  4Q LOSS WILD-TYPE   22   31
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           7                22
  CLUS_2           9                31
D45V5, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           6                26
  CLUS_2           6                13
  CLUS_3           6                37
D45V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV          4   14
  4Q LOSS WILD-TYPE    7   69
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           4                 7
  CLUS_2          14                69

Clustering(46) Variable = 5q loss
D46V1, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                28
  CLUS_2           1                35
  CLUS_3           4                29
D46V2, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                23
  CLUS_2           2                26
  CLUS_3           2                43
D46V3, multiclass
D46V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS CNV          2    2
  5Q LOSS WILD-TYPE   27   38
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           2                27
  CLUS_2           2                38
D46V5, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           2                30
  CLUS_2           2                17
  CLUS_3           1                42
D46V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS CNV          1    4
  5Q LOSS WILD-TYPE   10   79
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           1                10
  CLUS_2           4                79

Clustering(47) Variable = 6q loss
D47V1, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           8                20
  CLUS_2           6                30
  CLUS_3           6                27
D47V2, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           5                18
  CLUS_2           6                22
  CLUS_3           9                36
D47V3, multiclass
D47V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          8    5
  6Q LOSS WILD-TYPE   21   35
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           8                21
  CLUS_2           5                35
D47V5, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           6                26
  CLUS_2           3                16
  CLUS_3          10                33
D47V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          2   17
  6Q LOSS WILD-TYPE    9   66
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           2                 9
  CLUS_2          17                66

Clustering(48) Variable = 7p loss
D48V1, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1                27
  CLUS_2           0                36
  CLUS_3           4                29
D48V2, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1                22
  CLUS_2           2                26
  CLUS_3           2                43
D48V3, multiclass
D48V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS CNV          1    3
  7P LOSS WILD-TYPE   28   37
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1                28
  CLUS_2           3                37
D48V5, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1                31
  CLUS_2           1                18
  CLUS_3           3                40
D48V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS CNV          0    5
  7P LOSS WILD-TYPE   11   78
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           0                11
  CLUS_2           5                78

Clustering(49) Variable = 7q loss
D49V1, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           2                26
  CLUS_2           0                36
  CLUS_3           5                28
D49V2, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           2                21
  CLUS_2           2                26
  CLUS_3           3                42
D49V3, multiclass
D49V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS CNV          2    4
  7Q LOSS WILD-TYPE   27   36
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           2                27
  CLUS_2           4                36
D49V5, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           2                30
  CLUS_2           2                17
  CLUS_3           3                40
D49V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS CNV          2    5
  7Q LOSS WILD-TYPE    9   78
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           2                 9
  CLUS_2           5                78

Clustering(50) Variable = 8p loss
D50V1, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          16                12
  CLUS_2           7                29
  CLUS_3          18                15
D50V2, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           9                14
  CLUS_2          10                18
  CLUS_3          21                24
D50V3, multiclass
D50V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV         11   18
  8P LOSS WILD-TYPE   18   22
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          11                18
  CLUS_2          18                22
D50V5, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          12                20
  CLUS_2           8                11
  CLUS_3          20                23
D50V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV          6   34
  8P LOSS WILD-TYPE    5   49
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           6                 5
  CLUS_2          34                49

Clustering(51) Variable = 8q loss
D51V1, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           0                28
  CLUS_2           0                36
  CLUS_3           6                27
D51V2, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           0                23
  CLUS_2           2                26
  CLUS_3           4                41
D51V3, multiclass
D51V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS CNV          1    3
  8Q LOSS WILD-TYPE   28   37
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           1                28
  CLUS_2           3                37
D51V5, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           4                28
  CLUS_2           0                19
  CLUS_3           2                41
D51V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS CNV          0    6
  8Q LOSS WILD-TYPE   11   77
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           0                11
  CLUS_2           6                77

Clustering(52) Variable = 9p loss
D52V1, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           7                21
  CLUS_2           5                31
  CLUS_3           8                25
D52V2, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           4                19
  CLUS_2           7                21
  CLUS_3           9                36
D52V3, multiclass
D52V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV          8    8
  9P LOSS WILD-TYPE   21   32
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           8                21
  CLUS_2           8                32
D52V5, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           8                24
  CLUS_2           5                14
  CLUS_3           7                36
D52V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV          3   17
  9P LOSS WILD-TYPE    8   66
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           3                 8
  CLUS_2          17                66

Clustering(53) Variable = 9q loss
D53V1, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           7                21
  CLUS_2           5                31
  CLUS_3           7                26
D53V2, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           3                20
  CLUS_2           8                20
  CLUS_3           8                37
D53V3, multiclass
D53V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS CNV          7    8
  9Q LOSS WILD-TYPE   22   32
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           7                22
  CLUS_2           8                32
D53V5, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           7                25
  CLUS_2           4                15
  CLUS_3           7                36
D53V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS CNV          2   16
  9Q LOSS WILD-TYPE    9   67
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           2                 9
  CLUS_2          16                67

Clustering(54) Variable = 10p loss
D54V1, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            0                 28
  CLUS_2            2                 34
  CLUS_3            4                 29
D54V2, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            2                 26
  CLUS_3            3                 42
D54V3, multiclass
D54V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          2    2
  10P LOSS WILD-TYPE   27   38
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            2                 27
  CLUS_2            2                 38
D54V5, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            3                 29
  CLUS_2            1                 18
  CLUS_3            2                 41
D54V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          1    5
  10P LOSS WILD-TYPE   10   78
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                 10
  CLUS_2            5                 78

Clustering(55) Variable = 10q loss
D55V1, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            8                 28
  CLUS_3            8                 25
D55V2, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            6                 17
  CLUS_2            6                 22
  CLUS_3            5                 40
D55V3, multiclass
D55V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          8    5
  10Q LOSS WILD-TYPE   21   35
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            8                 21
  CLUS_2            5                 35
D55V5, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            8                 24
  CLUS_2            4                 15
  CLUS_3            5                 38
D55V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          4   13
  10Q LOSS WILD-TYPE    7   70
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            4                  7
  CLUS_2           13                 70

Clustering(56) Variable = 11p loss
D56V1, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            1                 35
  CLUS_3            4                 29
D56V2, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            3                 25
  CLUS_3            2                 43
D56V3, multiclass
D56V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV          3    2
  11P LOSS WILD-TYPE   26   38
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            3                 26
  CLUS_2            2                 38
D56V5, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            3                 29
  CLUS_2            1                 18
  CLUS_3            2                 41
D56V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV          1    5
  11P LOSS WILD-TYPE   10   78
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                 10
  CLUS_2            5                 78

Clustering(57) Variable = 11q loss
D57V1, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            2                 34
  CLUS_3            5                 28
D57V2, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            2                 21
  CLUS_2            2                 26
  CLUS_3            4                 41
D57V3, multiclass
D57V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV          6    2
  11Q LOSS WILD-TYPE   23   38
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            6                 23
  CLUS_2            2                 38
D57V5, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            2                 30
  CLUS_2            3                 16
  CLUS_3            3                 40
D57V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV          2    6
  11Q LOSS WILD-TYPE    9   77
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            2                  9
  CLUS_2            6                 77

Clustering(58) Variable = 12p loss
D58V1, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            3                 25
  CLUS_2            1                 35
  CLUS_3            4                 29
D58V2, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            0                 28
  CLUS_3            8                 37
D58V3, multiclass
D58V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS CNV          2    5
  12P LOSS WILD-TYPE   27   35
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            2                 27
  CLUS_2            5                 35
D58V5, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                 31
  CLUS_2            1                 18
  CLUS_3            5                 38
D58V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS CNV          1    6
  12P LOSS WILD-TYPE   10   77
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                 10
  CLUS_2            6                 77

Clustering(59) Variable = 13q loss
D59V1, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            5                 23
  CLUS_2            9                 27
  CLUS_3           16                 17
D59V2, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            5                 18
  CLUS_2           13                 15
  CLUS_3           12                 33
D59V3, multiclass
D59V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV         11   11
  13Q LOSS WILD-TYPE   18   29
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           11                 18
  CLUS_2           11                 29
D59V5, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           15                 17
  CLUS_2            5                 14
  CLUS_3            9                 34
D59V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          4   25
  13Q LOSS WILD-TYPE    7   58
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            4                  7
  CLUS_2           25                 58

Clustering(60) Variable = 14q loss
D60V1, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            6                 22
  CLUS_2            5                 31
  CLUS_3           15                 18
D60V2, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            5                 18
  CLUS_2           10                 18
  CLUS_3           11                 34
D60V3, multiclass
D60V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS CNV         11    8
  14Q LOSS WILD-TYPE   18   32
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           11                 18
  CLUS_2            8                 32
D60V5, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            9                 23
  CLUS_2            3                 16
  CLUS_3           13                 30
D60V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS CNV          3   22
  14Q LOSS WILD-TYPE    8   61
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            3                  8
  CLUS_2           22                 61

Clustering(61) Variable = 15q loss
D61V1, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            2                 26
  CLUS_2            0                 36
  CLUS_3            7                 26
D61V2, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            4                 24
  CLUS_3            4                 41
D61V3, multiclass
D61V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS CNV          4    3
  15Q LOSS WILD-TYPE   25   37
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            4                 25
  CLUS_2            3                 37
D61V5, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            3                 29
  CLUS_2            3                 16
  CLUS_3            3                 40
D61V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS CNV          2    7
  15Q LOSS WILD-TYPE    9   76
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            2                  9
  CLUS_2            7                 76

Clustering(62) Variable = 16p loss
D62V1, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            5                 23
  CLUS_2            4                 32
  CLUS_3           11                 22
D62V2, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            3                 20
  CLUS_2           11                 17
  CLUS_3            5                 40
D62V3, multiclass
D62V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS CNV         10    5
  16P LOSS WILD-TYPE   19   35
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1           10                 19
  CLUS_2            5                 35
D62V5, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1           10                 22
  CLUS_2            1                 18
  CLUS_3            8                 35
D62V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS CNV          1   18
  16P LOSS WILD-TYPE   10   65
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            1                 10
  CLUS_2           18                 65

Clustering(63) Variable = 16q loss
D63V1, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            6                 22
  CLUS_2            5                 31
  CLUS_3           16                 17
D63V2, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            1                 22
  CLUS_2           15                 13
  CLUS_3           10                 35
D63V3, multiclass
D63V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS CNV         13    9
  16Q LOSS WILD-TYPE   16   31
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           13                 16
  CLUS_2            9                 31
D63V5, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           10                 22
  CLUS_2            1                 18
  CLUS_3           15                 28
D63V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS CNV          0   26
  16Q LOSS WILD-TYPE   11   57
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            0                 11
  CLUS_2           26                 57

Clustering(64) Variable = 17p loss
D64V1, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           10                 18
  CLUS_2           10                 26
  CLUS_3           21                 12
D64V2, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            4                 19
  CLUS_2           14                 14
  CLUS_3           23                 22
D64V3, multiclass
D64V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV         12   19
  17P LOSS WILD-TYPE   17   21
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           12                 17
  CLUS_2           19                 21
D64V5, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           11                 21
  CLUS_2           12                  7
  CLUS_3           18                 25
D64V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV          9   32
  17P LOSS WILD-TYPE    2   51
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            9                  2
  CLUS_2           32                 51

Clustering(65) Variable = 17q loss
D65V1, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            2                 34
  CLUS_3            3                 30
D65V2, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            4                 24
  CLUS_3            2                 43
D65V3, multiclass
D65V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS CNV          1    3
  17Q LOSS WILD-TYPE   28   37
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            1                 28
  CLUS_2            3                 37
D65V5, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            3                 29
  CLUS_2            1                 18
  CLUS_3            2                 41
D65V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS CNV          1    5
  17Q LOSS WILD-TYPE   10   78
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            1                 10
  CLUS_2            5                 78

Clustering(66) Variable = 18p loss
D66V1, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            3                 33
  CLUS_3            6                 27
D66V2, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            6                 22
  CLUS_3            3                 42
D66V3, multiclass
D66V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV          4    4
  18P LOSS WILD-TYPE   25   36
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            4                 25
  CLUS_2            4                 36
D66V5, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            4                 28
  CLUS_2            1                 18
  CLUS_3            5                 38
D66V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV          1    9
  18P LOSS WILD-TYPE   10   74
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            1                 10
  CLUS_2            9                 74

Clustering(67) Variable = 18q loss
D67V1, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            2                 34
  CLUS_3            8                 25
D67V2, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            5                 23
  CLUS_3            5                 40
D67V3, multiclass
D67V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV          5    4
  18Q LOSS WILD-TYPE   24   36
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            5                 24
  CLUS_2            4                 36
D67V5, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            4                 28
  CLUS_2            1                 18
  CLUS_3            6                 37
D67V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV          1   10
  18Q LOSS WILD-TYPE   10   73
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            1                 10
  CLUS_2           10                 73

Clustering(68) Variable = 19p loss
D68V1, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            1                 35
  CLUS_3            3                 30
D68V2, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            3                 25
  CLUS_3            2                 43
D68V3, multiclass
D68V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS CNV          2    2
  19P LOSS WILD-TYPE   27   38
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            2                 27
  CLUS_2            2                 38
D68V5, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            2                 30
  CLUS_2            1                 18
  CLUS_3            2                 41
D68V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS CNV          1    4
  19P LOSS WILD-TYPE   10   79
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                 10
  CLUS_2            4                 79

Clustering(69) Variable = 20p loss
D69V1, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            2                 26
  CLUS_2            1                 35
  CLUS_3            2                 31
D69V2, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            2                 26
  CLUS_3            3                 42
D69V3, multiclass
[1] "Remove cluster labels:" "20P LOSS CNV"          
clus
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 2                 67 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A112         TCGA-BC-A216 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BC-A217         TCGA-BC-A3KF         TCGA-BC-A3KG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BD-A2L6         TCGA-CC-5258         TCGA-CC-5260 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-5262         TCGA-CC-5263         TCGA-CC-5264 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CC-A1HT         TCGA-CC-A3MB         TCGA-DD-A114 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11B         TCGA-DD-A11C 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1EA         TCGA-DD-A1EB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1ED         TCGA-DD-A1EE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EF         TCGA-DD-A1EG         TCGA-DD-A1EH 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DD-A39X         TCGA-DD-A39Y         TCGA-DD-A3A2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-ES-A2HS 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A23B         TCGA-FV-A2QQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FV-A3I1         TCGA-FV-A3R2         TCGA-FV-A3R3 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25X         TCGA-G3-A25Y 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CH         TCGA-G3-A3CJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G3-A3CK 
"20P LOSS WILD-TYPE" 
D69V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS CNV          1    1
  20P LOSS WILD-TYPE   28   39
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                 28
  CLUS_2            1                 39
D69V5, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            0                 32
  CLUS_2            3                 16
  CLUS_3            2                 41
D69V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS CNV          2    3
  20P LOSS WILD-TYPE    9   80
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            2                  9
  CLUS_2            3                 80

Clustering(70) Variable = 21q loss
D70V1, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            4                 24
  CLUS_2            4                 32
  CLUS_3            8                 25
D70V2, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            5                 18
  CLUS_2            3                 25
  CLUS_3            8                 37
D70V3, multiclass
D70V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV          5    4
  21Q LOSS WILD-TYPE   24   36
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            5                 24
  CLUS_2            4                 36
D70V5, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            3                 29
  CLUS_2            5                 14
  CLUS_3            8                 35
D70V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV          5   11
  21Q LOSS WILD-TYPE    6   72
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            5                  6
  CLUS_2           11                 72

Clustering(71) Variable = 22q loss
D71V1, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            1                 27
  CLUS_2            4                 32
  CLUS_3            5                 28
D71V2, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            4                 19
  CLUS_2            2                 26
  CLUS_3            4                 41
D71V3, multiclass
D71V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS CNV          6    3
  22Q LOSS WILD-TYPE   23   37
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            6                 23
  CLUS_2            3                 37
D71V5, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            4                 28
  CLUS_2            2                 17
  CLUS_3            4                 39
D71V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS CNV          2    8
  22Q LOSS WILD-TYPE    9   75
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            2                  9
  CLUS_2            8                 75
                     V1                      V2                      V3 
              "CN_CNMF"      "METHLYATION_CNMF"          "MRNASEQ_CNMF" 
                     V4                      V5                      V6 
"MRNASEQ_CHIERARCHICAL"           "MIRSEQ_CNMF"  "MIRSEQ_CHIERARCHICAL" 
> q(save="no")
