
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/SARC-TP/3472563/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/SARC-TP/3537675/SARC-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SARC-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=SARC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=63, in cluster file=52, common to both=52
[1] "Reduce the number of clustering variables from 80 to 65."
[1] 65 52
[1] "1p gain"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
                8                44 
      1P GAIN CNV 1P GAIN WILD-TYPE 
                8                44 
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                7                45 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                7                45 
[1] "2p gain"
[1] 3
      2P GAIN CNV 2P GAIN WILD-TYPE 
                3                49 
      2P GAIN CNV 2P GAIN WILD-TYPE 
                3                49 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
                5                47 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                5                47 
[1] "5p gain"
[1] 3
      5P GAIN CNV 5P GAIN WILD-TYPE 
               13                39 
      5P GAIN CNV 5P GAIN WILD-TYPE 
               13                39 
[1] "5q gain"
[1] 3
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               11                41 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               11                41 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
                8                44 
      6P GAIN CNV 6P GAIN WILD-TYPE 
                8                44 
[1] "6q gain"
[1] 3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
               10                42 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
               10                42 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
               13                39 
      7P GAIN CNV 7P GAIN WILD-TYPE 
               13                39 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               11                41 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               11                41 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
                9                43 
      8P GAIN CNV 8P GAIN WILD-TYPE 
                9                43 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                8                44 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                8                44 
[1] "9p gain"
[1] 3
      9P GAIN CNV 9P GAIN WILD-TYPE 
                4                48 
      9P GAIN CNV 9P GAIN WILD-TYPE 
                4                48 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                7                45 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                7                45 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 7                 45 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 7                 45 
[1] "14q gain"
[1] 3
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 3                 49 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 3                 49 
[1] "15q gain"
[1] 3
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 8                 44 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 8                 44 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 7                 45 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 7                 45 
[1] "17p gain"
[1] 3
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 8                 44 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 8                 44 
[1] "17q gain"
[1] 3
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                 6                 46 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                 6                 46 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 7                 45 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 7                 45 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 8                 44 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 8                 44 
[1] "19p gain"
[1] 3
      19P GAIN CNV 19P GAIN WILD-TYPE 
                10                 42 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                10                 42 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 6                 46 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 6                 46 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                13                 39 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                13                 39 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                16                 36 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                16                 36 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 7                 45 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 7                 45 
[1] "22q gain"
[1] 3
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 5                 47 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 5                 47 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
                9                43 
      1P LOSS CNV 1P LOSS WILD-TYPE 
                9                43 
[1] "1q loss"
[1] 3
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                6                46 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                6                46 
[1] "2p loss"
[1] 3
      2P LOSS CNV 2P LOSS WILD-TYPE 
               10                42 
      2P LOSS CNV 2P LOSS WILD-TYPE 
               10                42 
[1] "2q loss"
[1] 3
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                8                44 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                8                44 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
               10                42 
      3P LOSS CNV 3P LOSS WILD-TYPE 
               10                42 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
               13                39 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
               13                39 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
                6                46 
      4P LOSS CNV 4P LOSS WILD-TYPE 
                6                46 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                6                46 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                6                46 
[1] "5p loss"
[1] 3
      5P LOSS CNV 5P LOSS WILD-TYPE 
                4                48 
      5P LOSS CNV 5P LOSS WILD-TYPE 
                4                48 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                5                47 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                5                47 
[1] "6p loss"
[1] 3
      6P LOSS CNV 6P LOSS WILD-TYPE 
                8                44 
      6P LOSS CNV 6P LOSS WILD-TYPE 
                8                44 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                4                48 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                4                48 
[1] "7p loss"
[1] 3
      7P LOSS CNV 7P LOSS WILD-TYPE 
                4                48 
      7P LOSS CNV 7P LOSS WILD-TYPE 
                4                48 
[1] "7q loss"
[1] 3
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                6                46 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                6                46 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
               10                42 
      8P LOSS CNV 8P LOSS WILD-TYPE 
               10                42 
[1] "8q loss"
[1] 3
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                5                47 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                5                47 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
               11                41 
      9P LOSS CNV 9P LOSS WILD-TYPE 
               11                41 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                6                46 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                6                46 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                18                 34 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                18                 34 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                20                 32 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                20                 32 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                17                 35 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                17                 35 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                13                 39 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                13                 39 
[1] "12q loss"
[1] 3
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 5                 47 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 5                 47 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                23                 29 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                23                 29 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                16                 36 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                16                 36 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 9                 43 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 9                 43 
[1] "16p loss"
[1] 3
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 9                 43 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 9                 43 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                20                 32 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                20                 32 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
                 8                 44 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                 8                 44 
[1] "17q loss"
[1] 3
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 5                 47 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 5                 47 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 8                 44 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 8                 44 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                10                 42 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                10                 42 
[1] "19q loss"
[1] 3
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 5                 47 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 5                 47 
[1] "20p loss"
[1] 3
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 5                 47 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 5                 47 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 8                 44 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 8                 44 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                15                 37 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                15                 37 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
               10                42 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
               10                42 
[1] "data2feature, selection="
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[5] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 6 rows and 52 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:'MIRSEQ_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'MIRSEQ_MATURE_CNMF':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
[1] "CN_CNMF"                     "METHLYATION_CNMF"           
[3] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[5] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 52 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
MIRSEQ_CNMF, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=2, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain
D1V1, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           3                16
  CLUS_2           0                12
  CLUS_3           5                16
D1V2, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           1                15
  CLUS_2           2                16
  CLUS_3           5                13
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN CNV          1    2
  1P GAIN WILD-TYPE   15   11
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           1                15
  CLUS_2           2                11
D1V4, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           2                10
  CLUS_3           1                15
D1V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN CNV          1    2
  1P GAIN WILD-TYPE   15   11
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           1                15
  CLUS_2           2                11
D1V6, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           2                10
  CLUS_3           1                15

Clustering(2) Variable = 1q gain
D2V1, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           3                16
  CLUS_2           0                12
  CLUS_3           4                17
D2V2, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           1                15
  CLUS_2           0                18
  CLUS_3           6                12
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN CNV          0    3
  1Q GAIN WILD-TYPE   16   10
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           0                16
  CLUS_2           3                10
D2V4, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           3                 9
  CLUS_3           0                16
D2V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN CNV          0    3
  1Q GAIN WILD-TYPE   16   10
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           0                16
  CLUS_2           3                10
D2V6, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           3                 9
  CLUS_3           0                16

Clustering(3) Variable = 2p gain
D3V1, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           2                17
  CLUS_2           1                11
  CLUS_3           0                21
D3V2, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           0                16
  CLUS_2           3                15
  CLUS_3           0                18
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN CNV          1    0
  2P GAIN WILD-TYPE   15   13
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           1                15
  CLUS_2           0                13
D3V4, multiclass
[1] "Remove cluster labels:" "2P GAIN CNV"           
clus
      2P GAIN CNV 2P GAIN WILD-TYPE 
                1                28 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DX-A3LS        TCGA-DX-A3LT        TCGA-DX-A3LU        TCGA-DX-A3LW 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DX-A3M1        TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A3NJ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FX-A3NK        TCGA-FX-A3RE        TCGA-FX-A3TO        TCGA-HB-A2OT 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-HB-A3L4        TCGA-IE-A3OV        TCGA-IF-A3RQ        TCGA-IS-A3K6 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-IS-A3K7        TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
D3V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN CNV          1    0
  2P GAIN WILD-TYPE   15   13
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           1                15
  CLUS_2           0                13
D3V6, multiclass
[1] "Remove cluster labels:" "2P GAIN CNV"           
clus
      2P GAIN CNV 2P GAIN WILD-TYPE 
                1                28 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DX-A3LS        TCGA-DX-A3LT        TCGA-DX-A3LU        TCGA-DX-A3LW 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DX-A3M1        TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A3NJ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FX-A3NK        TCGA-FX-A3RE        TCGA-FX-A3TO        TCGA-HB-A2OT 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-HB-A3L4        TCGA-IE-A3OV        TCGA-IF-A3RQ        TCGA-IS-A3K6 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-IS-A3K7        TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 

Clustering(4) Variable = 4p gain
D4V1, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           2                17
  CLUS_2           2                10
  CLUS_3           1                20
D4V2, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           1                15
  CLUS_2           3                15
  CLUS_3           1                17
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN CNV          0    0
  4P GAIN WILD-TYPE   16   13
D4V4, multiclass
D4V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN CNV          0    0
  4P GAIN WILD-TYPE   16   13
D4V6, multiclass

Clustering(5) Variable = 5p gain
D5V1, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           9                10
  CLUS_2           1                11
  CLUS_3           3                18
D5V2, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           4                12
  CLUS_2           5                13
  CLUS_3           4                14
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV          3    2
  5P GAIN WILD-TYPE   13   11
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           3                13
  CLUS_2           2                11
D5V4, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           2                10
  CLUS_3           3                13
D5V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV          3    2
  5P GAIN WILD-TYPE   13   11
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           3                13
  CLUS_2           2                11
D5V6, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           2                10
  CLUS_3           3                13

Clustering(6) Variable = 5q gain
D6V1, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           8                11
  CLUS_2           1                11
  CLUS_3           2                19
D6V2, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           2                14
  CLUS_2           6                12
  CLUS_3           3                15
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN CNV          3    2
  5Q GAIN WILD-TYPE   13   11
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           3                13
  CLUS_2           2                11
D6V4, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           2                10
  CLUS_3           3                13
D6V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN CNV          3    2
  5Q GAIN WILD-TYPE   13   11
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           3                13
  CLUS_2           2                11
D6V6, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           2                10
  CLUS_3           3                13

Clustering(7) Variable = 6p gain
D7V1, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           4                15
  CLUS_2           3                 9
  CLUS_3           1                20
D7V2, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           4                12
  CLUS_2           4                14
  CLUS_3           0                18
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV          4    0
  6P GAIN WILD-TYPE   12   13
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           4                12
  CLUS_2           0                13
D7V4, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           0                12
  CLUS_3           4                12
D7V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV          4    0
  6P GAIN WILD-TYPE   12   13
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           4                12
  CLUS_2           0                13
D7V6, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           0                12
  CLUS_3           4                12

Clustering(8) Variable = 6q gain
D8V1, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           3                16
  CLUS_2           6                 6
  CLUS_3           1                20
D8V2, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           4                12
  CLUS_2           6                12
  CLUS_3           0                18
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV          5    0
  6Q GAIN WILD-TYPE   11   13
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           5                11
  CLUS_2           0                13
D8V4, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           0                12
  CLUS_3           5                11
D8V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV          5    0
  6Q GAIN WILD-TYPE   11   13
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           5                11
  CLUS_2           0                13
D8V6, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           0                12
  CLUS_3           5                11

Clustering(9) Variable = 7p gain
D9V1, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           9                10
  CLUS_2           2                10
  CLUS_3           2                19
D9V2, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           5                11
  CLUS_2           6                12
  CLUS_3           2                16
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN CNV          2    3
  7P GAIN WILD-TYPE   14   10
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           2                14
  CLUS_2           3                10
D9V4, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           1                 0
  CLUS_2           2                10
  CLUS_3           2                14
D9V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN CNV          2    3
  7P GAIN WILD-TYPE   14   10
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           2                14
  CLUS_2           3                10
D9V6, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           1                 0
  CLUS_2           2                10
  CLUS_3           2                14

Clustering(10) Variable = 7q gain
D10V1, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           7                12
  CLUS_2           2                10
  CLUS_3           2                19
D10V2, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           4                12
  CLUS_2           6                12
  CLUS_3           1                17
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV          2    3
  7Q GAIN WILD-TYPE   14   10
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           2                14
  CLUS_2           3                10
D10V4, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           1                 0
  CLUS_2           2                10
  CLUS_3           2                14
D10V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV          2    3
  7Q GAIN WILD-TYPE   14   10
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           2                14
  CLUS_2           3                10
D10V6, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           1                 0
  CLUS_2           2                10
  CLUS_3           2                14

Clustering(11) Variable = 8p gain
D11V1, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           6                13
  CLUS_2           0                12
  CLUS_3           3                18
D11V2, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           2                14
  CLUS_2           4                14
  CLUS_3           3                15
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV          2    3
  8P GAIN WILD-TYPE   14   10
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           2                14
  CLUS_2           3                10
D11V4, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           3                 9
  CLUS_3           2                14
D11V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV          2    3
  8P GAIN WILD-TYPE   14   10
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           2                14
  CLUS_2           3                10
D11V6, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           3                 9
  CLUS_3           2                14

Clustering(12) Variable = 8q gain
D12V1, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           5                14
  CLUS_2           0                12
  CLUS_3           3                18
D12V2, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           0                16
  CLUS_2           4                14
  CLUS_3           4                14
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV          2    2
  8Q GAIN WILD-TYPE   14   11
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           2                14
  CLUS_2           2                11
D12V4, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           2                10
  CLUS_3           2                14
D12V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV          2    2
  8Q GAIN WILD-TYPE   14   11
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           2                14
  CLUS_2           2                11
D12V6, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           2                10
  CLUS_3           2                14

Clustering(13) Variable = 9p gain
D13V1, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1                18
  CLUS_2           3                 9
  CLUS_3           0                21
D13V2, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2                14
  CLUS_2           2                16
  CLUS_3           0                18
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN CNV          2    0
  9P GAIN WILD-TYPE   14   13
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2                14
  CLUS_2           0                13
D13V4, multiclass
[1] "Remove cluster labels:" "9P GAIN CNV"           
clus
      9P GAIN CNV 9P GAIN WILD-TYPE 
                2                27 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DX-A3LS        TCGA-DX-A3LT        TCGA-DX-A3LW        TCGA-DX-A3M1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A2QS        TCGA-FX-A3NJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FX-A3NK        TCGA-FX-A3RE        TCGA-HB-A2OT        TCGA-HB-A3L4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IE-A3OV        TCGA-IF-A3RQ        TCGA-IS-A3K6        TCGA-IS-A3K7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4        TCGA-IW-A3M5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D13V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN CNV          2    0
  9P GAIN WILD-TYPE   14   13
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2                14
  CLUS_2           0                13
D13V6, multiclass
[1] "Remove cluster labels:" "9P GAIN CNV"           
clus
      9P GAIN CNV 9P GAIN WILD-TYPE 
                2                27 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DX-A3LS        TCGA-DX-A3LT        TCGA-DX-A3LW        TCGA-DX-A3M1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A2QS        TCGA-FX-A3NJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FX-A3NK        TCGA-FX-A3RE        TCGA-HB-A2OT        TCGA-HB-A3L4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IE-A3OV        TCGA-IF-A3RQ        TCGA-IS-A3K6        TCGA-IS-A3K7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4        TCGA-IW-A3M5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 

Clustering(14) Variable = 9q gain
D14V1, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           3                16
  CLUS_2           4                 8
  CLUS_3           0                21
D14V2, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                14
  CLUS_2           4                14
  CLUS_3           1                17
D14V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN CNV          4    0
  9Q GAIN WILD-TYPE   12   13
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           4                12
  CLUS_2           0                13
D14V4, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           0                12
  CLUS_3           4                12
D14V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN CNV          4    0
  9Q GAIN WILD-TYPE   12   13
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           4                12
  CLUS_2           0                13
D14V6, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           0                12
  CLUS_3           4                12

Clustering(15) Variable = 12p gain
D15V1, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            4                 15
  CLUS_2            1                 11
  CLUS_3            2                 19
D15V2, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            3                 15
  CLUS_3            2                 16
D15V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN CNV          1    0
  12P GAIN WILD-TYPE   15   13
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            0                 13
D15V4, multiclass
[1] "Remove cluster labels:" "12P GAIN CNV"          
clus
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 1                 28 
        TCGA-DX-A2IZ         TCGA-DX-A2J0         TCGA-DX-A2J1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DX-A2J4         TCGA-DX-A3LT         TCGA-DX-A3LU 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DX-A3LW         TCGA-DX-A3M1         TCGA-DX-A3M2 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DX-A3U5         TCGA-FX-A2QS         TCGA-FX-A3NJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FX-A3NK         TCGA-FX-A3RE         TCGA-FX-A3TO 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-HB-A2OT         TCGA-HB-A3L4         TCGA-IE-A3OV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IF-A3RQ         TCGA-IS-A3K6         TCGA-IS-A3K7 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IS-A3K8         TCGA-IS-A3KA         TCGA-IW-A3M4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IW-A3M5         TCGA-IW-A3M6         TCGA-K1-A3PN 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-K1-A3PO 
"12P GAIN WILD-TYPE" 
D15V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN CNV          1    0
  12P GAIN WILD-TYPE   15   13
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            0                 13
D15V6, multiclass
[1] "Remove cluster labels:" "12P GAIN CNV"          
clus
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 1                 28 
        TCGA-DX-A2IZ         TCGA-DX-A2J0         TCGA-DX-A2J1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DX-A2J4         TCGA-DX-A3LT         TCGA-DX-A3LU 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DX-A3LW         TCGA-DX-A3M1         TCGA-DX-A3M2 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DX-A3U5         TCGA-FX-A2QS         TCGA-FX-A3NJ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FX-A3NK         TCGA-FX-A3RE         TCGA-FX-A3TO 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-HB-A2OT         TCGA-HB-A3L4         TCGA-IE-A3OV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IF-A3RQ         TCGA-IS-A3K6         TCGA-IS-A3K7 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IS-A3K8         TCGA-IS-A3KA         TCGA-IW-A3M4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IW-A3M5         TCGA-IW-A3M6         TCGA-K1-A3PN 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-K1-A3PO 
"12P GAIN WILD-TYPE" 

Clustering(16) Variable = 14q gain
D16V1, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            1                 18
  CLUS_2            1                 11
  CLUS_3            1                 20
D16V2, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            0                 16
  CLUS_2            2                 16
  CLUS_3            1                 17
D16V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN CNV          1    0
  14Q GAIN WILD-TYPE   15   13
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            0                 13
D16V4, multiclass
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 1                 28 
        TCGA-DX-A2IZ         TCGA-DX-A2J0         TCGA-DX-A2J1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DX-A2J4         TCGA-DX-A3LS         TCGA-DX-A3LT 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DX-A3LU         TCGA-DX-A3LW         TCGA-DX-A3M1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DX-A3M2         TCGA-DX-A3U5         TCGA-FX-A2QS 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FX-A3NJ         TCGA-FX-A3NK         TCGA-FX-A3RE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FX-A3TO         TCGA-HB-A2OT         TCGA-HB-A3L4 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IE-A3OV         TCGA-IF-A3RQ         TCGA-IS-A3K6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IS-A3K7         TCGA-IS-A3K8         TCGA-IS-A3KA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IW-A3M4         TCGA-IW-A3M6         TCGA-K1-A3PN 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-K1-A3PO 
"14Q GAIN WILD-TYPE" 
D16V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN CNV          1    0
  14Q GAIN WILD-TYPE   15   13
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            0                 13
D16V6, multiclass
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 1                 28 
        TCGA-DX-A2IZ         TCGA-DX-A2J0         TCGA-DX-A2J1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DX-A2J4         TCGA-DX-A3LS         TCGA-DX-A3LT 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DX-A3LU         TCGA-DX-A3LW         TCGA-DX-A3M1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DX-A3M2         TCGA-DX-A3U5         TCGA-FX-A2QS 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FX-A3NJ         TCGA-FX-A3NK         TCGA-FX-A3RE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FX-A3TO         TCGA-HB-A2OT         TCGA-HB-A3L4 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IE-A3OV         TCGA-IF-A3RQ         TCGA-IS-A3K6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IS-A3K7         TCGA-IS-A3K8         TCGA-IS-A3KA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IW-A3M4         TCGA-IW-A3M6         TCGA-K1-A3PN 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-K1-A3PO 
"14Q GAIN WILD-TYPE" 

Clustering(17) Variable = 15q gain
D17V1, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            4                 15
  CLUS_2            0                 12
  CLUS_3            4                 17
D17V2, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            2                 16
  CLUS_3            4                 14
D17V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN CNV          1    1
  15Q GAIN WILD-TYPE   15   12
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            1                 12
D17V4, multiclass
[1] "Remove cluster labels:" "15Q GAIN CNV"          
clus
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 2                 27 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DX-A3LS         TCGA-DX-A3LT         TCGA-DX-A3LU 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DX-A3LW         TCGA-DX-A3M1         TCGA-DX-A3M2 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DX-A3U5         TCGA-FX-A2QS         TCGA-FX-A3NJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FX-A3NK         TCGA-FX-A3RE         TCGA-FX-A3TO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HB-A2OT         TCGA-HB-A3L4         TCGA-IE-A3OV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IF-A3RQ         TCGA-IS-A3K6         TCGA-IS-A3K7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IS-A3K8         TCGA-IW-A3M4         TCGA-IW-A3M5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D17V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN CNV          1    1
  15Q GAIN WILD-TYPE   15   12
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            1                 12
D17V6, multiclass
[1] "Remove cluster labels:" "15Q GAIN CNV"          
clus
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 2                 27 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DX-A3LS         TCGA-DX-A3LT         TCGA-DX-A3LU 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DX-A3LW         TCGA-DX-A3M1         TCGA-DX-A3M2 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DX-A3U5         TCGA-FX-A2QS         TCGA-FX-A3NJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FX-A3NK         TCGA-FX-A3RE         TCGA-FX-A3TO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HB-A2OT         TCGA-HB-A3L4         TCGA-IE-A3OV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IF-A3RQ         TCGA-IS-A3K6         TCGA-IS-A3K7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IS-A3K8         TCGA-IW-A3M4         TCGA-IW-A3M5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 

Clustering(18) Variable = 16p gain
D18V1, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            2                 17
  CLUS_2            1                 11
  CLUS_3            4                 17
D18V2, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            0                 16
  CLUS_2            4                 14
  CLUS_3            3                 15
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV          1    2
  16P GAIN WILD-TYPE   15   11
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            2                 11
D18V4, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            2                 10
  CLUS_3            1                 15
D18V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV          1    2
  16P GAIN WILD-TYPE   15   11
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            2                 11
D18V6, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            2                 10
  CLUS_3            1                 15

Clustering(19) Variable = 17p gain
D19V1, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            6                 13
  CLUS_2            2                 10
  CLUS_3            0                 21
D19V2, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            7                 11
  CLUS_3            0                 18
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN CNV          1    1
  17P GAIN WILD-TYPE   15   12
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            1                 12
D19V4, multiclass
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 2                 27 
        TCGA-DX-A2IZ         TCGA-DX-A2J0         TCGA-DX-A2J1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DX-A2J4         TCGA-DX-A3LS         TCGA-DX-A3LT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DX-A3LU         TCGA-DX-A3LW         TCGA-DX-A3M1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DX-A3M2         TCGA-DX-A3U5         TCGA-FX-A2QS 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FX-A3NJ         TCGA-FX-A3NK         TCGA-HB-A2OT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HB-A3L4         TCGA-IE-A3OV         TCGA-IF-A3RQ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IS-A3K6         TCGA-IS-A3K7         TCGA-IS-A3K8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IS-A3KA         TCGA-IW-A3M4         TCGA-IW-A3M5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D19V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN CNV          1    1
  17P GAIN WILD-TYPE   15   12
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            1                 12
D19V6, multiclass
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 2                 27 
        TCGA-DX-A2IZ         TCGA-DX-A2J0         TCGA-DX-A2J1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DX-A2J4         TCGA-DX-A3LS         TCGA-DX-A3LT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DX-A3LU         TCGA-DX-A3LW         TCGA-DX-A3M1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DX-A3M2         TCGA-DX-A3U5         TCGA-FX-A2QS 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FX-A3NJ         TCGA-FX-A3NK         TCGA-HB-A2OT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HB-A3L4         TCGA-IE-A3OV         TCGA-IF-A3RQ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IS-A3K6         TCGA-IS-A3K7         TCGA-IS-A3K8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IS-A3KA         TCGA-IW-A3M4         TCGA-IW-A3M5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 

Clustering(20) Variable = 17q gain
D20V1, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            4                 15
  CLUS_2            1                 11
  CLUS_3            1                 20
D20V2, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            4                 14
  CLUS_3            1                 17
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN CNV          1    2
  17Q GAIN WILD-TYPE   15   11
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            2                 11
D20V4, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            1                  0
  CLUS_2            1                 11
  CLUS_3            1                 15
D20V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN CNV          1    2
  17Q GAIN WILD-TYPE   15   11
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            2                 11
D20V6, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            1                  0
  CLUS_2            1                 11
  CLUS_3            1                 15

Clustering(21) Variable = 18p gain
D21V1, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            3                 16
  CLUS_2            1                 11
  CLUS_3            3                 18
D21V2, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            4                 14
  CLUS_3            2                 16
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          1    1
  18P GAIN WILD-TYPE   15   12
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            1                 12
D21V4, multiclass
[1] "Remove cluster labels:" "18P GAIN CNV"          
clus
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 2                 27 
        TCGA-DX-A2IZ         TCGA-DX-A2J0         TCGA-DX-A2J1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DX-A2J4         TCGA-DX-A3LS         TCGA-DX-A3LT 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DX-A3LU         TCGA-DX-A3LW         TCGA-DX-A3M1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DX-A3M2         TCGA-DX-A3U5         TCGA-FX-A2QS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FX-A3NJ         TCGA-FX-A3NK         TCGA-FX-A3RE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-HB-A2OT         TCGA-HB-A3L4         TCGA-IE-A3OV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IF-A3RQ         TCGA-IS-A3K6         TCGA-IS-A3K7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IS-A3K8         TCGA-IW-A3M4         TCGA-IW-A3M5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
D21V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          1    1
  18P GAIN WILD-TYPE   15   12
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            1                 12
D21V6, multiclass
[1] "Remove cluster labels:" "18P GAIN CNV"          
clus
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 2                 27 
        TCGA-DX-A2IZ         TCGA-DX-A2J0         TCGA-DX-A2J1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DX-A2J4         TCGA-DX-A3LS         TCGA-DX-A3LT 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DX-A3LU         TCGA-DX-A3LW         TCGA-DX-A3M1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DX-A3M2         TCGA-DX-A3U5         TCGA-FX-A2QS 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FX-A3NJ         TCGA-FX-A3NK         TCGA-FX-A3RE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-HB-A2OT         TCGA-HB-A3L4         TCGA-IE-A3OV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IF-A3RQ         TCGA-IS-A3K6         TCGA-IS-A3K7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IS-A3K8         TCGA-IW-A3M4         TCGA-IW-A3M5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 

Clustering(22) Variable = 18q gain
D22V1, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            5                 14
  CLUS_2            0                 12
  CLUS_3            3                 18
D22V2, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            4                 14
  CLUS_3            2                 16
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          2    1
  18Q GAIN WILD-TYPE   14   12
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            1                 12
D22V4, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            1                 11
  CLUS_3            2                 14
D22V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          2    1
  18Q GAIN WILD-TYPE   14   12
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            1                 12
D22V6, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            1                 11
  CLUS_3            2                 14

Clustering(23) Variable = 19p gain
D23V1, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            8                 11
  CLUS_2            1                 11
  CLUS_3            1                 20
D23V2, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            5                 13
  CLUS_3            3                 15
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN CNV          1    2
  19P GAIN WILD-TYPE   15   11
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            2                 11
D23V4, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                  0
  CLUS_2            1                 11
  CLUS_3            1                 15
D23V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN CNV          1    2
  19P GAIN WILD-TYPE   15   11
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            2                 11
D23V6, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                  0
  CLUS_2            1                 11
  CLUS_3            1                 15

Clustering(24) Variable = 19q gain
D24V1, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            5                 14
  CLUS_2            1                 11
  CLUS_3            0                 21
D24V2, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            3                 15
  CLUS_3            1                 17
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN CNV          0    0
  19Q GAIN WILD-TYPE   16   13
D24V4, multiclass
D24V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN CNV          0    0
  19Q GAIN WILD-TYPE   16   13
D24V6, multiclass

Clustering(25) Variable = 20p gain
D25V1, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            7                 12
  CLUS_2            2                 10
  CLUS_3            4                 17
D25V2, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            7                 11
  CLUS_3            4                 14
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV          2    2
  20P GAIN WILD-TYPE   14   11
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            2                 11
D25V4, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            2                 10
  CLUS_3            2                 14
D25V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV          2    2
  20P GAIN WILD-TYPE   14   11
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            2                 11
D25V6, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            2                 10
  CLUS_3            2                 14

Clustering(26) Variable = 20q gain
D26V1, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            9                 10
  CLUS_2            4                  8
  CLUS_3            3                 18
D26V2, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            3                 13
  CLUS_2           10                  8
  CLUS_3            3                 15
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV          3    2
  20Q GAIN WILD-TYPE   13   11
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            2                 11
D26V4, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            2                 10
  CLUS_3            3                 13
D26V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV          3    2
  20Q GAIN WILD-TYPE   13   11
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            2                 11
D26V6, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            2                 10
  CLUS_3            3                 13

Clustering(27) Variable = 21q gain
D27V1, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            3                 16
  CLUS_2            2                 10
  CLUS_3            2                 19
D27V2, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            5                 13
  CLUS_3            1                 17
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN CNV          1    1
  21Q GAIN WILD-TYPE   15   12
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            1                 12
D27V4, multiclass
[1] "Remove cluster labels:" "21Q GAIN CNV"          
clus
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 2                 27 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DX-A3LS         TCGA-DX-A3LT         TCGA-DX-A3LU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DX-A3LW         TCGA-DX-A3M1         TCGA-DX-A3M2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DX-A3U5         TCGA-FX-A2QS         TCGA-FX-A3NJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FX-A3NK         TCGA-FX-A3RE         TCGA-FX-A3TO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-HB-A2OT         TCGA-HB-A3L4         TCGA-IF-A3RQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IS-A3K6         TCGA-IS-A3K7         TCGA-IS-A3K8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IS-A3KA         TCGA-IW-A3M4         TCGA-IW-A3M5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D27V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN CNV          1    1
  21Q GAIN WILD-TYPE   15   12
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            1                 12
D27V6, multiclass
[1] "Remove cluster labels:" "21Q GAIN CNV"          
clus
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 2                 27 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DX-A3LS         TCGA-DX-A3LT         TCGA-DX-A3LU 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DX-A3LW         TCGA-DX-A3M1         TCGA-DX-A3M2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DX-A3U5         TCGA-FX-A2QS         TCGA-FX-A3NJ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FX-A3NK         TCGA-FX-A3RE         TCGA-FX-A3TO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-HB-A2OT         TCGA-HB-A3L4         TCGA-IF-A3RQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IS-A3K6         TCGA-IS-A3K7         TCGA-IS-A3K8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IS-A3KA         TCGA-IW-A3M4         TCGA-IW-A3M5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 

Clustering(28) Variable = 22q gain
D28V1, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            3                 16
  CLUS_2            0                 12
  CLUS_3            2                 19
D28V2, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            1                 17
  CLUS_3            2                 16
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN CNV          0    1
  22Q GAIN WILD-TYPE   16   12
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            0                 16
  CLUS_2            1                 12
D28V4, multiclass
[1] "Remove cluster labels:" "22Q GAIN CNV"          
clus
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 1                 28 
        TCGA-DX-A2IZ         TCGA-DX-A2J0         TCGA-DX-A2J1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DX-A2J4         TCGA-DX-A3LS         TCGA-DX-A3LT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DX-A3LU         TCGA-DX-A3LW         TCGA-DX-A3M1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DX-A3M2         TCGA-DX-A3U5         TCGA-FX-A2QS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FX-A3NJ         TCGA-FX-A3NK         TCGA-FX-A3RE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FX-A3TO         TCGA-HB-A3L4         TCGA-IE-A3OV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IF-A3RQ         TCGA-IS-A3K6         TCGA-IS-A3K7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IS-A3K8         TCGA-IS-A3KA         TCGA-IW-A3M4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IW-A3M5         TCGA-IW-A3M6         TCGA-K1-A3PN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-K1-A3PO 
"22Q GAIN WILD-TYPE" 
D28V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN CNV          0    1
  22Q GAIN WILD-TYPE   16   12
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            0                 16
  CLUS_2            1                 12
D28V6, multiclass
[1] "Remove cluster labels:" "22Q GAIN CNV"          
clus
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 1                 28 
        TCGA-DX-A2IZ         TCGA-DX-A2J0         TCGA-DX-A2J1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DX-A2J4         TCGA-DX-A3LS         TCGA-DX-A3LT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DX-A3LU         TCGA-DX-A3LW         TCGA-DX-A3M1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DX-A3M2         TCGA-DX-A3U5         TCGA-FX-A2QS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FX-A3NJ         TCGA-FX-A3NK         TCGA-FX-A3RE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FX-A3TO         TCGA-HB-A3L4         TCGA-IE-A3OV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IF-A3RQ         TCGA-IS-A3K6         TCGA-IS-A3K7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IS-A3K8         TCGA-IS-A3KA         TCGA-IW-A3M4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IW-A3M5         TCGA-IW-A3M6         TCGA-K1-A3PN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-K1-A3PO 
"22Q GAIN WILD-TYPE" 

Clustering(29) Variable = 1p loss
D29V1, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           6                13
  CLUS_2           1                11
  CLUS_3           2                19
D29V2, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1                15
  CLUS_2           3                15
  CLUS_3           5                13
D29V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS CNV          1    4
  1P LOSS WILD-TYPE   15    9
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1                15
  CLUS_2           4                 9
D29V4, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1                 0
  CLUS_2           3                 9
  CLUS_3           1                15
D29V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS CNV          1    4
  1P LOSS WILD-TYPE   15    9
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1                15
  CLUS_2           4                 9
D29V6, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1                 0
  CLUS_2           3                 9
  CLUS_3           1                15

Clustering(30) Variable = 1q loss
D30V1, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           3                16
  CLUS_2           2                10
  CLUS_3           1                20
D30V2, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           2                16
  CLUS_3           2                16
D30V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS CNV          2    1
  1Q LOSS WILD-TYPE   14   12
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           1                12
D30V4, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           1                11
  CLUS_3           2                14
D30V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS CNV          2    1
  1Q LOSS WILD-TYPE   14   12
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           1                12
D30V6, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           1                11
  CLUS_3           2                14

Clustering(31) Variable = 2p loss
D31V1, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           4                15
  CLUS_2           2                10
  CLUS_3           4                17
D31V2, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1                15
  CLUS_2           4                14
  CLUS_3           5                13
D31V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS CNV          2    3
  2P LOSS WILD-TYPE   14   10
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           3                10
D31V4, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           3                 9
  CLUS_3           2                14
D31V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS CNV          2    3
  2P LOSS WILD-TYPE   14   10
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           3                10
D31V6, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           3                 9
  CLUS_3           2                14

Clustering(32) Variable = 2q loss
D32V1, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           4                15
  CLUS_2           2                10
  CLUS_3           2                19
D32V2, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1                15
  CLUS_2           4                14
  CLUS_3           3                15
D32V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS CNV          2    2
  2Q LOSS WILD-TYPE   14   11
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           2                11
D32V4, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           2                10
  CLUS_3           2                14
D32V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS CNV          2    2
  2Q LOSS WILD-TYPE   14   11
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           2                11
D32V6, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           2                10
  CLUS_3           2                14

Clustering(33) Variable = 3p loss
D33V1, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           3                16
  CLUS_2           5                 7
  CLUS_3           2                19
D33V2, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           4                12
  CLUS_2           4                14
  CLUS_3           2                16
D33V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          4    0
  3P LOSS WILD-TYPE   12   13
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           4                12
  CLUS_2           0                13
D33V4, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           0                12
  CLUS_3           4                12
D33V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          4    0
  3P LOSS WILD-TYPE   12   13
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           4                12
  CLUS_2           0                13
D33V6, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           0                12
  CLUS_3           4                12

Clustering(34) Variable = 3q loss
D34V1, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           3                16
  CLUS_2           7                 5
  CLUS_3           3                18
D34V2, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           3                13
  CLUS_2           7                11
  CLUS_3           3                15
D34V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS CNV          5    1
  3Q LOSS WILD-TYPE   11   12
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           5                11
  CLUS_2           1                12
D34V4, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           1                11
  CLUS_3           5                11
D34V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS CNV          5    1
  3Q LOSS WILD-TYPE   11   12
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           5                11
  CLUS_2           1                12
D34V6, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           1                11
  CLUS_3           5                11

Clustering(35) Variable = 4p loss
D35V1, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           4                15
  CLUS_2           0                12
  CLUS_3           2                19
D35V2, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           0                16
  CLUS_2           3                15
  CLUS_3           3                15
D35V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV          2    0
  4P LOSS WILD-TYPE   14   13
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           0                13
D35V4, multiclass
[1] "Remove cluster labels:" "4P LOSS CNV"           
clus
      4P LOSS CNV 4P LOSS WILD-TYPE 
                2                27 
       TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4        TCGA-DX-A3LS 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DX-A3LT        TCGA-DX-A3LU        TCGA-DX-A3LW        TCGA-DX-A3M1 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A2QS        TCGA-FX-A3NJ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FX-A3NK        TCGA-FX-A3RE        TCGA-FX-A3TO        TCGA-HB-A2OT 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-HB-A3L4        TCGA-IE-A3OV        TCGA-IF-A3RQ        TCGA-IS-A3K6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-IS-A3K7        TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D35V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV          2    0
  4P LOSS WILD-TYPE   14   13
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           0                13
D35V6, multiclass
[1] "Remove cluster labels:" "4P LOSS CNV"           
clus
      4P LOSS CNV 4P LOSS WILD-TYPE 
                2                27 
       TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4        TCGA-DX-A3LS 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DX-A3LT        TCGA-DX-A3LU        TCGA-DX-A3LW        TCGA-DX-A3M1 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A2QS        TCGA-FX-A3NJ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FX-A3NK        TCGA-FX-A3RE        TCGA-FX-A3TO        TCGA-HB-A2OT 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-HB-A3L4        TCGA-IE-A3OV        TCGA-IF-A3RQ        TCGA-IS-A3K6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-IS-A3K7        TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 

Clustering(36) Variable = 4q loss
D36V1, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           3                16
  CLUS_2           0                12
  CLUS_3           3                18
D36V2, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           0                16
  CLUS_2           3                15
  CLUS_3           3                15
D36V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV          2    0
  4Q LOSS WILD-TYPE   14   13
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           0                13
D36V4, multiclass
[1] "Remove cluster labels:" "4Q LOSS CNV"           
clus
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                2                27 
       TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4        TCGA-DX-A3LS 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DX-A3LT        TCGA-DX-A3LU        TCGA-DX-A3LW        TCGA-DX-A3M1 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A2QS        TCGA-FX-A3NJ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FX-A3NK        TCGA-FX-A3RE        TCGA-FX-A3TO        TCGA-HB-A2OT 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HB-A3L4        TCGA-IE-A3OV        TCGA-IF-A3RQ        TCGA-IS-A3K6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-IS-A3K7        TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
D36V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV          2    0
  4Q LOSS WILD-TYPE   14   13
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           0                13
D36V6, multiclass
[1] "Remove cluster labels:" "4Q LOSS CNV"           
clus
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                2                27 
       TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4        TCGA-DX-A3LS 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DX-A3LT        TCGA-DX-A3LU        TCGA-DX-A3LW        TCGA-DX-A3M1 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A2QS        TCGA-FX-A3NJ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FX-A3NK        TCGA-FX-A3RE        TCGA-FX-A3TO        TCGA-HB-A2OT 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HB-A3L4        TCGA-IE-A3OV        TCGA-IF-A3RQ        TCGA-IS-A3K6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-IS-A3K7        TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 

Clustering(37) Variable = 5p loss
D37V1, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2                17
  CLUS_2           2                10
  CLUS_3           0                21
D37V2, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1                15
  CLUS_2           2                16
  CLUS_3           1                17
D37V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS CNV          2    0
  5P LOSS WILD-TYPE   14   13
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           0                13
D37V4, multiclass
[1] "Remove cluster labels:" "5P LOSS CNV"           
clus
      5P LOSS CNV 5P LOSS WILD-TYPE 
                2                27 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DX-A3LS        TCGA-DX-A3LU        TCGA-DX-A3LW        TCGA-DX-A3M1 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A2QS        TCGA-FX-A3NJ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FX-A3NK        TCGA-FX-A3RE        TCGA-FX-A3TO        TCGA-HB-A2OT 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-HB-A3L4        TCGA-IE-A3OV        TCGA-IF-A3RQ        TCGA-IS-A3K6 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4        TCGA-IW-A3M5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
D37V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS CNV          2    0
  5P LOSS WILD-TYPE   14   13
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           0                13
D37V6, multiclass
[1] "Remove cluster labels:" "5P LOSS CNV"           
clus
      5P LOSS CNV 5P LOSS WILD-TYPE 
                2                27 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DX-A3LS        TCGA-DX-A3LU        TCGA-DX-A3LW        TCGA-DX-A3M1 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A2QS        TCGA-FX-A3NJ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FX-A3NK        TCGA-FX-A3RE        TCGA-FX-A3TO        TCGA-HB-A2OT 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-HB-A3L4        TCGA-IE-A3OV        TCGA-IF-A3RQ        TCGA-IS-A3K6 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4        TCGA-IW-A3M5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 

Clustering(38) Variable = 5q loss
D38V1, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           2                17
  CLUS_2           2                10
  CLUS_3           1                20
D38V2, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                16
  CLUS_2           3                15
  CLUS_3           2                16
D38V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS CNV          2    0
  5Q LOSS WILD-TYPE   14   13
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           0                13
D38V4, multiclass
[1] "Remove cluster labels:" "5Q LOSS CNV"           
clus
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                2                27 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DX-A3LS        TCGA-DX-A3LU        TCGA-DX-A3LW        TCGA-DX-A3M1 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A3NJ        TCGA-FX-A3NK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FX-A3RE        TCGA-FX-A3TO        TCGA-HB-A2OT        TCGA-HB-A3L4 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IE-A3OV        TCGA-IF-A3RQ        TCGA-IS-A3K6        TCGA-IS-A3K7 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4        TCGA-IW-A3M5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
D38V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS CNV          2    0
  5Q LOSS WILD-TYPE   14   13
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           0                13
D38V6, multiclass
[1] "Remove cluster labels:" "5Q LOSS CNV"           
clus
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                2                27 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DX-A3LS        TCGA-DX-A3LU        TCGA-DX-A3LW        TCGA-DX-A3M1 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A3NJ        TCGA-FX-A3NK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FX-A3RE        TCGA-FX-A3TO        TCGA-HB-A2OT        TCGA-HB-A3L4 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IE-A3OV        TCGA-IF-A3RQ        TCGA-IS-A3K6        TCGA-IS-A3K7 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4        TCGA-IW-A3M5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 

Clustering(39) Variable = 6p loss
D39V1, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           2                17
  CLUS_2           2                10
  CLUS_3           4                17
D39V2, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1                15
  CLUS_2           2                16
  CLUS_3           5                13
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS CNV          2    4
  6P LOSS WILD-TYPE   14    9
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           4                 9
D39V4, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           4                 8
  CLUS_3           2                14
D39V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS CNV          2    4
  6P LOSS WILD-TYPE   14    9
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           2                14
  CLUS_2           4                 9
D39V6, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           4                 8
  CLUS_3           2                14

Clustering(40) Variable = 6q loss
D40V1, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           2                17
  CLUS_2           0                12
  CLUS_3           2                19
D40V2, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           0                16
  CLUS_2           1                17
  CLUS_3           3                15
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          1    1
  6Q LOSS WILD-TYPE   15   12
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           1                15
  CLUS_2           1                12
D40V4, multiclass
[1] "Remove cluster labels:" "6Q LOSS CNV"           
clus
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                2                27 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DX-A3LS        TCGA-DX-A3LT        TCGA-DX-A3LU        TCGA-DX-A3LW 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DX-A3M1        TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A2QS 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FX-A3NJ        TCGA-FX-A3NK        TCGA-FX-A3RE        TCGA-HB-A2OT 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-HB-A3L4        TCGA-IF-A3RQ        TCGA-IS-A3K6        TCGA-IS-A3K7 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4        TCGA-IW-A3M5 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
D40V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          1    1
  6Q LOSS WILD-TYPE   15   12
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           1                15
  CLUS_2           1                12
D40V6, multiclass
[1] "Remove cluster labels:" "6Q LOSS CNV"           
clus
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                2                27 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DX-A3LS        TCGA-DX-A3LT        TCGA-DX-A3LU        TCGA-DX-A3LW 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DX-A3M1        TCGA-DX-A3M2        TCGA-DX-A3U5        TCGA-FX-A2QS 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FX-A3NJ        TCGA-FX-A3NK        TCGA-FX-A3RE        TCGA-HB-A2OT 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-HB-A3L4        TCGA-IF-A3RQ        TCGA-IS-A3K6        TCGA-IS-A3K7 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-IS-A3K8        TCGA-IS-A3KA        TCGA-IW-A3M4        TCGA-IW-A3M5 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-IW-A3M6        TCGA-K1-A3PN        TCGA-K1-A3PO 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 

Clustering(41) Variable = 7p loss
D41V1, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           3                16
  CLUS_2           0                12
  CLUS_3           1                20
D41V2, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           0                16
  CLUS_2           1                17
  CLUS_3           3                15
D41V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS CNV          1    2
  7P LOSS WILD-TYPE   15   11
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1                15
  CLUS_2           2                11
D41V4, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           2                10
  CLUS_3           1                15
D41V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS CNV          1    2
  7P LOSS WILD-TYPE   15   11
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1                15
  CLUS_2           2                11
D41V6, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           2                10
  CLUS_3           1                15

Clustering(42) Variable = 7q loss
D42V1, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           4                15
  CLUS_2           1                11
  CLUS_3           1                20
D42V2, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           0                16
  CLUS_2           3                15
  CLUS_3           3                15
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS CNV          3    1
  7Q LOSS WILD-TYPE   13   12
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           3                13
  CLUS_2           1                12
D42V4, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           1                11
  CLUS_3           3                13
D42V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS CNV          3    1
  7Q LOSS WILD-TYPE   13   12
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           3                13
  CLUS_2           1                12
D42V6, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           1                11
  CLUS_3           3                13

Clustering(43) Variable = 8p loss
D43V1, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           5                14
  CLUS_2           3                 9
  CLUS_3           2                19
D43V2, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           5                11
  CLUS_2           3                15
  CLUS_3           2                16
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV          4    2
  8P LOSS WILD-TYPE   12   11
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           4                12
  CLUS_2           2                11
D43V4, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           1                 0
  CLUS_2           1                11
  CLUS_3           4                12
D43V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV          4    2
  8P LOSS WILD-TYPE   12   11
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           4                12
  CLUS_2           2                11
D43V6, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           1                 0
  CLUS_2           1                11
  CLUS_3           4                12

Clustering(44) Variable = 8q loss
D44V1, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           1                18
  CLUS_2           2                10
  CLUS_3           2                19
D44V2, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           4                12
  CLUS_2           0                18
  CLUS_3           1                17
D44V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS CNV          3    0
  8Q LOSS WILD-TYPE   13   13
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           3                13
  CLUS_2           0                13
D44V4, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           0                12
  CLUS_3           3                13
D44V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS CNV          3    0
  8Q LOSS WILD-TYPE   13   13
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           3                13
  CLUS_2           0                13
D44V6, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           0                12
  CLUS_3           3                13

Clustering(45) Variable = 9p loss
D45V1, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           9                10
  CLUS_2           1                11
  CLUS_3           1                20
D45V2, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           3                13
  CLUS_2           6                12
  CLUS_3           2                16
D45V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV          5    1
  9P LOSS WILD-TYPE   11   12
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           5                11
  CLUS_2           1                12
D45V4, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           1                 0
  CLUS_2           0                12
  CLUS_3           5                11
D45V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV          5    1
  9P LOSS WILD-TYPE   11   12
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           5                11
  CLUS_2           1                12
D45V6, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           1                 0
  CLUS_2           0                12
  CLUS_3           5                11

Clustering(46) Variable = 9q loss
D46V1, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           4                15
  CLUS_2           0                12
  CLUS_3           2                19
D46V2, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           3                13
  CLUS_2           2                16
  CLUS_3           1                17
D46V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS CNV          3    1
  9Q LOSS WILD-TYPE   13   12
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           3                13
  CLUS_2           1                12
D46V4, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           1                11
  CLUS_3           3                13
D46V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS CNV          3    1
  9Q LOSS WILD-TYPE   13   12
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           3                13
  CLUS_2           1                12
D46V6, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           1                11
  CLUS_3           3                13

Clustering(47) Variable = 10p loss
D47V1, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           10                  9
  CLUS_2            2                 10
  CLUS_3            6                 15
D47V2, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            8                 10
  CLUS_3            8                 10
D47V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          4    4
  10P LOSS WILD-TYPE   12    9
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            4                 12
  CLUS_2            4                  9
D47V4, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                  0
  CLUS_2            3                  9
  CLUS_3            4                 12
D47V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          4    4
  10P LOSS WILD-TYPE   12    9
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            4                 12
  CLUS_2            4                  9
D47V6, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                  0
  CLUS_2            3                  9
  CLUS_3            4                 12

Clustering(48) Variable = 10q loss
D48V1, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            8                 11
  CLUS_2            1                 11
  CLUS_3           11                 10
D48V2, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            7                 11
  CLUS_3           11                  7
D48V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          3    7
  10Q LOSS WILD-TYPE   13    6
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            7                  6
D48V4, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                  0
  CLUS_2            6                  6
  CLUS_3            3                 13
D48V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          3    7
  10Q LOSS WILD-TYPE   13    6
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            7                  6
D48V6, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                  0
  CLUS_2            6                  6
  CLUS_3            3                 13

Clustering(49) Variable = 11p loss
D49V1, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            7                 12
  CLUS_2            7                  5
  CLUS_3            3                 18
D49V2, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            9                  9
  CLUS_3            5                 13
D49V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV          5    2
  11P LOSS WILD-TYPE   11   11
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            5                 11
  CLUS_2            2                 11
D49V4, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                  0
  CLUS_2            1                 11
  CLUS_3            5                 11
D49V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV          5    2
  11P LOSS WILD-TYPE   11   11
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            5                 11
  CLUS_2            2                 11
D49V6, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                  0
  CLUS_2            1                 11
  CLUS_3            5                 11

Clustering(50) Variable = 11q loss
D50V1, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            5                 14
  CLUS_2            7                  5
  CLUS_3            1                 20
D50V2, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            7                 11
  CLUS_3            3                 15
D50V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV          5    1
  11Q LOSS WILD-TYPE   11   12
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            5                 11
  CLUS_2            1                 12
D50V4, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            1                 11
  CLUS_3            5                 11
D50V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV          5    1
  11Q LOSS WILD-TYPE   11   12
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            5                 11
  CLUS_2            1                 12
D50V6, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            1                 11
  CLUS_3            5                 11

Clustering(51) Variable = 12q loss
D51V1, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            1                 18
  CLUS_2            1                 11
  CLUS_3            3                 18
D51V2, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            2                 16
  CLUS_3            1                 17
D51V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS CNV          2    0
  12Q LOSS WILD-TYPE   14   13
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            0                 13
D51V4, multiclass
[1] "Remove cluster labels:" "12Q LOSS CNV"          
clus
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 2                 27 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DX-A3LT         TCGA-DX-A3LU         TCGA-DX-A3LW 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DX-A3M1         TCGA-DX-A3M2         TCGA-DX-A3U5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3NK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FX-A3RE         TCGA-FX-A3TO         TCGA-HB-A2OT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-HB-A3L4         TCGA-IE-A3OV         TCGA-IF-A3RQ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IS-A3K6         TCGA-IS-A3K7         TCGA-IS-A3K8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IS-A3KA         TCGA-IW-A3M4         TCGA-IW-A3M5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
D51V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS CNV          2    0
  12Q LOSS WILD-TYPE   14   13
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            0                 13
D51V6, multiclass
[1] "Remove cluster labels:" "12Q LOSS CNV"          
clus
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 2                 27 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DX-A3LT         TCGA-DX-A3LU         TCGA-DX-A3LW 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DX-A3M1         TCGA-DX-A3M2         TCGA-DX-A3U5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3NK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FX-A3RE         TCGA-FX-A3TO         TCGA-HB-A2OT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-HB-A3L4         TCGA-IE-A3OV         TCGA-IF-A3RQ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IS-A3K6         TCGA-IS-A3K7         TCGA-IS-A3K8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IS-A3KA         TCGA-IW-A3M4         TCGA-IW-A3M5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 

Clustering(52) Variable = 13q loss
D52V1, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           12                  7
  CLUS_2            5                  7
  CLUS_3            6                 15
D52V2, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            5                 11
  CLUS_2           10                  8
  CLUS_3            8                 10
D52V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          6    6
  13Q LOSS WILD-TYPE   10    7
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            6                 10
  CLUS_2            6                  7
D52V4, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            1                  0
  CLUS_2            5                  7
  CLUS_3            6                 10
D52V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          6    6
  13Q LOSS WILD-TYPE   10    7
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            6                 10
  CLUS_2            6                  7
D52V6, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            1                  0
  CLUS_2            5                  7
  CLUS_3            6                 10

Clustering(53) Variable = 14q loss
D53V1, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            9                 10
  CLUS_2            4                  8
  CLUS_3            3                 18
D53V2, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            6                 10
  CLUS_2            3                 15
  CLUS_3            7                 11
D53V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS CNV          3    6
  14Q LOSS WILD-TYPE   13    7
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            6                  7
D53V4, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            6                  6
  CLUS_3            3                 13
D53V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS CNV          3    6
  14Q LOSS WILD-TYPE   13    7
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            6                  7
D53V6, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            6                  6
  CLUS_3            3                 13

Clustering(54) Variable = 15q loss
D54V1, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            4                 15
  CLUS_2            4                  8
  CLUS_3            1                 20
D54V2, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            5                 13
  CLUS_3            1                 17
D54V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS CNV          7    0
  15Q LOSS WILD-TYPE    9   13
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            7                  9
  CLUS_2            0                 13
D54V4, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            0                 12
  CLUS_3            7                  9
D54V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS CNV          7    0
  15Q LOSS WILD-TYPE    9   13
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            7                  9
  CLUS_2            0                 13
D54V6, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            0                 12
  CLUS_3            7                  9

Clustering(55) Variable = 16p loss
D55V1, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            4                 15
  CLUS_2            3                  9
  CLUS_3            2                 19
D55V2, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            4                 14
  CLUS_3            3                 15
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS CNV          4    1
  16P LOSS WILD-TYPE   12   12
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            4                 12
  CLUS_2            1                 12
D55V4, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            1                 11
  CLUS_3            4                 12
D55V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS CNV          4    1
  16P LOSS WILD-TYPE   12   12
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            4                 12
  CLUS_2            1                 12
D55V6, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            1                 11
  CLUS_3            4                 12

Clustering(56) Variable = 16q loss
D56V1, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            7                 12
  CLUS_2            6                  6
  CLUS_3            7                 14
D56V2, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            8                 10
  CLUS_3           10                  8
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS CNV          4    5
  16Q LOSS WILD-TYPE   12    8
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            4                 12
  CLUS_2            5                  8
D56V4, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            1                  0
  CLUS_2            4                  8
  CLUS_3            4                 12
D56V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS CNV          4    5
  16Q LOSS WILD-TYPE   12    8
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            4                 12
  CLUS_2            5                  8
D56V6, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            1                  0
  CLUS_2            4                  8
  CLUS_3            4                 12

Clustering(57) Variable = 17p loss
D57V1, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            2                 17
  CLUS_2            2                 10
  CLUS_3            4                 17
D57V2, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            2                 16
  CLUS_3            5                 13
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV          3    3
  17P LOSS WILD-TYPE   13   10
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            3                 10
D57V4, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            3                  9
  CLUS_3            3                 13
D57V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV          3    3
  17P LOSS WILD-TYPE   13   10
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            3                 10
D57V6, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            3                  9
  CLUS_3            3                 13

Clustering(58) Variable = 17q loss
D58V1, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            1                 18
  CLUS_2            1                 11
  CLUS_3            3                 18
D58V2, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            0                 16
  CLUS_2            1                 17
  CLUS_3            4                 14
D58V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS CNV          1    2
  17Q LOSS WILD-TYPE   15   11
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            2                 11
D58V4, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            2                 10
  CLUS_3            1                 15
D58V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS CNV          1    2
  17Q LOSS WILD-TYPE   15   11
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            2                 11
D58V6, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            2                 10
  CLUS_3            1                 15

Clustering(59) Variable = 18p loss
D59V1, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            2                 17
  CLUS_2            3                  9
  CLUS_3            3                 18
D59V2, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            5                 13
  CLUS_3            2                 16
D59V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV          3    1
  18P LOSS WILD-TYPE   13   12
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            1                 12
D59V4, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            1                 11
  CLUS_3            3                 13
D59V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV          3    1
  18P LOSS WILD-TYPE   13   12
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            1                 12
D59V6, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            1                 11
  CLUS_3            3                 13

Clustering(60) Variable = 18q loss
D60V1, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            4                 15
  CLUS_2            3                  9
  CLUS_3            3                 18
D60V2, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            2                 14
  CLUS_2            5                 13
  CLUS_3            3                 15
D60V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV          3    1
  18Q LOSS WILD-TYPE   13   12
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            1                 12
D60V4, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            1                 11
  CLUS_3            3                 13
D60V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV          3    1
  18Q LOSS WILD-TYPE   13   12
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            1                 12
D60V6, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            1                 11
  CLUS_3            3                 13

Clustering(61) Variable = 19q loss
D61V1, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            1                 18
  CLUS_2            2                 10
  CLUS_3            2                 19
D61V2, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            0                 16
  CLUS_2            2                 16
  CLUS_3            3                 15
D61V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS CNV          1    1
  19Q LOSS WILD-TYPE   15   12
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            1                 12
D61V4, multiclass
[1] "Remove cluster labels:" "19Q LOSS CNV"          
clus
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 2                 27 
        TCGA-DX-A2IZ         TCGA-DX-A2J1         TCGA-DX-A2J4 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A3LS         TCGA-DX-A3LT         TCGA-DX-A3LU 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A3LW         TCGA-DX-A3M1         TCGA-DX-A3M2 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A3U5         TCGA-FX-A2QS         TCGA-FX-A3NJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FX-A3NK         TCGA-FX-A3RE         TCGA-FX-A3TO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HB-A2OT         TCGA-HB-A3L4         TCGA-IE-A3OV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IF-A3RQ         TCGA-IS-A3K6         TCGA-IS-A3K7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IS-A3K8         TCGA-IS-A3KA         TCGA-IW-A3M5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D61V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS CNV          1    1
  19Q LOSS WILD-TYPE   15   12
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            1                 12
D61V6, multiclass
[1] "Remove cluster labels:" "19Q LOSS CNV"          
clus
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 2                 27 
        TCGA-DX-A2IZ         TCGA-DX-A2J1         TCGA-DX-A2J4 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A3LS         TCGA-DX-A3LT         TCGA-DX-A3LU 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A3LW         TCGA-DX-A3M1         TCGA-DX-A3M2 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A3U5         TCGA-FX-A2QS         TCGA-FX-A3NJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FX-A3NK         TCGA-FX-A3RE         TCGA-FX-A3TO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HB-A2OT         TCGA-HB-A3L4         TCGA-IE-A3OV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IF-A3RQ         TCGA-IS-A3K6         TCGA-IS-A3K7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IS-A3K8         TCGA-IS-A3KA         TCGA-IW-A3M5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IW-A3M6         TCGA-K1-A3PN         TCGA-K1-A3PO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 

Clustering(62) Variable = 20p loss
D62V1, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                 18
  CLUS_2            3                  9
  CLUS_3            1                 20
D62V2, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                 15
  CLUS_2            3                 15
  CLUS_3            1                 17
D62V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS CNV          4    1
  20P LOSS WILD-TYPE   12   12
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            4                 12
  CLUS_2            1                 12
D62V4, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            1                 11
  CLUS_3            4                 12
D62V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS CNV          4    1
  20P LOSS WILD-TYPE   12   12
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            4                 12
  CLUS_2            1                 12
D62V6, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            1                 11
  CLUS_3            4                 12

Clustering(63) Variable = 21q loss
D63V1, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            5                 14
  CLUS_2            3                  9
  CLUS_3            0                 21
D63V2, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            3                 15
  CLUS_3            2                 16
D63V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV          3    2
  21Q LOSS WILD-TYPE   13   11
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            2                 11
D63V4, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            2                 10
  CLUS_3            3                 13
D63V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV          3    2
  21Q LOSS WILD-TYPE   13   11
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            2                 11
D63V6, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            2                 10
  CLUS_3            3                 13

Clustering(64) Variable = 22q loss
D64V1, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            6                 13
  CLUS_2            3                  9
  CLUS_3            6                 15
D64V2, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            3                 13
  CLUS_2            5                 13
  CLUS_3            7                 11
D64V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS CNV          7    4
  22Q LOSS WILD-TYPE    9    9
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            7                  9
  CLUS_2            4                  9
D64V4, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            4                  8
  CLUS_3            7                  9
D64V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS CNV          7    4
  22Q LOSS WILD-TYPE    9    9
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            7                  9
  CLUS_2            4                  9
D64V6, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            0                  1
  CLUS_2            4                  8
  CLUS_3            7                  9

Clustering(65) Variable = Xq loss
D65V1, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           6                13
  CLUS_2           3                 9
  CLUS_3           1                20
D65V2, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1                15
  CLUS_2           6                12
  CLUS_3           3                15
D65V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS CNV          3    3
  XQ LOSS WILD-TYPE   13   10
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3                13
  CLUS_2           3                10
D65V4, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           3                 9
  CLUS_3           3                13
D65V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS CNV          3    3
  XQ LOSS WILD-TYPE   13   10
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3                13
  CLUS_2           3                10
D65V6, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                 1
  CLUS_2           3                 9
  CLUS_3           3                13
                           V1                            V2 
                    "CN_CNMF"            "METHLYATION_CNMF" 
                           V3                            V4 
                "MIRSEQ_CNMF"        "MIRSEQ_CHIERARCHICAL" 
                           V5                            V6 
         "MIRSEQ_MATURE_CNMF" "MIRSEQ_MATURE_CHIERARCHICAL" 
> q(save="no")
