
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/UCEC-TP/3472756/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/UCEC-TP/3538590/UCEC-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=UCEC-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=UCEC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=500, in cluster file=492, common to both=492
[1] "Reduce the number of clustering variables from 80 to 79."
[1]  79 492
[1] "1p gain"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
               21               471 
      1P GAIN CNV 1P GAIN WILD-TYPE 
               21               471 
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
              138               354 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
              138               354 
[1] "2p gain"
[1] 3
      2P GAIN CNV 2P GAIN WILD-TYPE 
               51               441 
      2P GAIN CNV 2P GAIN WILD-TYPE 
               51               441 
[1] "2q gain"
[1] 3
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               40               452 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               40               452 
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
               28               464 
      3P GAIN CNV 3P GAIN WILD-TYPE 
               28               464 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               50               442 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               50               442 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
                6               486 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                6               486 
[1] "5p gain"
[1] 3
      5P GAIN CNV 5P GAIN WILD-TYPE 
               32               460 
      5P GAIN CNV 5P GAIN WILD-TYPE 
               32               460 
[1] "5q gain"
[1] 3
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                9               483 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                9               483 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
               38               454 
      6P GAIN CNV 6P GAIN WILD-TYPE 
               38               454 
[1] "6q gain"
[1] 3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
               30               462 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
               30               462 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
               43               449 
      7P GAIN CNV 7P GAIN WILD-TYPE 
               43               449 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               43               449 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               43               449 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
               86               406 
      8P GAIN CNV 8P GAIN WILD-TYPE 
               86               406 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
              118               374 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
              118               374 
[1] "9p gain"
[1] 3
      9P GAIN CNV 9P GAIN WILD-TYPE 
               14               478 
      9P GAIN CNV 9P GAIN WILD-TYPE 
               14               478 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                4               488 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                4               488 
[1] "10p gain"
[1] 3
      10P GAIN CNV 10P GAIN WILD-TYPE 
                87                405 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                87                405 
[1] "10q gain"
[1] 3
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                79                413 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                79                413 
[1] "11p gain"
[1] 3
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 8                484 
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 8                484 
[1] "11q gain"
[1] 3
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 8                484 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 8                484 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                37                455 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                37                455 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                28                464 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                28                464 
[1] "13q gain"
[1] 3
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                20                472 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                20                472 
[1] "14q gain"
[1] 3
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                20                472 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                20                472 
[1] "15q gain"
[1] 3
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 6                486 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 6                486 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                12                480 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                12                480 
[1] "16q gain"
[1] 3
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 4                488 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 4                488 
[1] "17p gain"
[1] 3
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 7                485 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 7                485 
[1] "17q gain"
[1] 3
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                13                479 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                13                479 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                37                455 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                37                455 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                20                472 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                20                472 
[1] "19p gain"
[1] 3
      19P GAIN CNV 19P GAIN WILD-TYPE 
                31                461 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                31                461 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                28                464 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                28                464 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                65                427 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                65                427 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                78                414 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                78                414 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                25                467 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                25                467 
[1] "22q gain"
[1] 3
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 9                483 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 9                483 
[1] "Xq gain"
[1] 3
      XQ GAIN CNV XQ GAIN WILD-TYPE 
               12               480 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
               12               480 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
               13               479 
      1P LOSS CNV 1P LOSS WILD-TYPE 
               13               479 
[1] "1q loss"
[1] 3
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                4               488 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                4               488 
[1] "2p loss"
[1] 3
      2P LOSS CNV 2P LOSS WILD-TYPE 
                6               486 
      2P LOSS CNV 2P LOSS WILD-TYPE 
                6               486 
[1] "2q loss"
[1] 3
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                8               484 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                8               484 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
               31               461 
      3P LOSS CNV 3P LOSS WILD-TYPE 
               31               461 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
               12               480 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
               12               480 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
               66               426 
      4P LOSS CNV 4P LOSS WILD-TYPE 
               66               426 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               64               428 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               64               428 
[1] "5p loss"
[1] 3
      5P LOSS CNV 5P LOSS WILD-TYPE 
               27               465 
      5P LOSS CNV 5P LOSS WILD-TYPE 
               27               465 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               45               447 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               45               447 
[1] "6p loss"
[1] 3
      6P LOSS CNV 6P LOSS WILD-TYPE 
               10               482 
      6P LOSS CNV 6P LOSS WILD-TYPE 
               10               482 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               12               480 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               12               480 
[1] "7p loss"
[1] 3
      7P LOSS CNV 7P LOSS WILD-TYPE 
               29               463 
      7P LOSS CNV 7P LOSS WILD-TYPE 
               29               463 
[1] "7q loss"
[1] 3
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
               27               465 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
               27               465 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
               53               439 
      8P LOSS CNV 8P LOSS WILD-TYPE 
               53               439 
[1] "8q loss"
[1] 3
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
               12               480 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
               12               480 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
               76               416 
      9P LOSS CNV 9P LOSS WILD-TYPE 
               76               416 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               93               399 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               93               399 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                23                469 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                23                469 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                24                468 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                24                468 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                53                439 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                53                439 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                45                447 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                45                447 
[1] "12p loss"
[1] 3
      12P LOSS CNV 12P LOSS WILD-TYPE 
                25                467 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                25                467 
[1] "12q loss"
[1] 3
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                18                474 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                18                474 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                60                432 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                60                432 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                42                450 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                42                450 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                81                411 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                81                411 
[1] "16p loss"
[1] 3
      16P LOSS CNV 16P LOSS WILD-TYPE 
                69                423 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                69                423 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
               110                382 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
               110                382 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
               105                387 
      17P LOSS CNV 17P LOSS WILD-TYPE 
               105                387 
[1] "17q loss"
[1] 3
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                68                424 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                68                424 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                36                456 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                36                456 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                49                443 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                49                443 
[1] "19p loss"
[1] 3
      19P LOSS CNV 19P LOSS WILD-TYPE 
                34                458 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                34                458 
[1] "19q loss"
[1] 3
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                28                464 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                28                464 
[1] "20p loss"
[1] 3
      20P LOSS CNV 20P LOSS WILD-TYPE 
                15                477 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                15                477 
[1] "20q loss"
[1] 3
      20Q LOSS CNV 20Q LOSS WILD-TYPE 
                 7                485 
      20Q LOSS CNV 20Q LOSS WILD-TYPE 
                 7                485 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                32                460 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                32                460 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                87                405 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                87                405 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
               18               474 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
               18               474 
[1] "data2feature, selection="
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"

Input Data has 12 rows and 492 columns.

Variable 1:'MRNA_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 2:'MRNA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 3:'CN_CNMF':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MIRSEQ_MATURE_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MIRSEQ_MATURE_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "MRNA_CNMF"                   "MRNA_CHIERARCHICAL"         
 [3] "CN_CNMF"                     "METHLYATION_CNMF"           
 [5] "RPPA_CNMF"                   "RPPA_CHIERARCHICAL"         
 [7] "MRNASEQ_CNMF"                "MRNASEQ_CHIERARCHICAL"      
 [9] "MIRSEQ_CNMF"                 "MIRSEQ_CHIERARCHICAL"       
[11] "MIRSEQ_MATURE_CNMF"          "MIRSEQ_MATURE_CHIERARCHICAL"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 492 columns, 0 survival variables, and 12 non-survival variables.
MRNA_CNMF, nv=4, binary=FALSE, numeric=FALSE
MRNA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
CN_CNMF, nv=5, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=6, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=2, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_MATURE_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain
D1V1, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           2                12
  CLUS_2           1                16
  CLUS_3           0                12
  CLUS_4           0                10
D1V2, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           2                17
  CLUS_2           0                19
  CLUS_3           1                14
D1V3, multiclass
D1V4, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           8               135
  CLUS_2           4                80
  CLUS_3           5               145
D1V5, multiclass
D1V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN CNV          3    2
  1P GAIN WILD-TYPE  118   71
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           3               118
  CLUS_2           2                71
D1V7, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           7               135
  CLUS_2           1               106
  CLUS_3           3               110
D1V8, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           1                64
  CLUS_2           1                91
  CLUS_3           4                61
  CLUS_4           5               135
D1V9, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          15               192
  CLUS_2           1               143
  CLUS_3           5               127
D1V10, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           5               188
  CLUS_2           2                77
  CLUS_3           0                27
  CLUS_4          14               170
D1V11, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          12               157
  CLUS_2           3               113
  CLUS_3           2                72
D1V12, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           4               113
  CLUS_2          13               184
  CLUS_3           0                45

Clustering(2) Variable = 1q gain
D2V1, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           8                 6
  CLUS_2           5                12
  CLUS_3           5                 7
  CLUS_4           2                 8
D2V2, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          10                 9
  CLUS_2           6                13
  CLUS_3           4                11
D2V3, multiclass
D2V4, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          24               119
  CLUS_2          19                65
  CLUS_3          49               101
D2V5, multiclass
D2V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN CNV         48   12
  1Q GAIN WILD-TYPE   73   61
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          48                73
  CLUS_2          12                61
D2V7, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          24               118
  CLUS_2          26                81
  CLUS_3          51                62
D2V8, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          26                39
  CLUS_2          24                68
  CLUS_3          31                34
  CLUS_4          20               120
D2V9, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          41               166
  CLUS_2          35               109
  CLUS_3          62                70
D2V10, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          64               129
  CLUS_2          29                50
  CLUS_3           6                21
  CLUS_4          39               145
D2V11, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          39               130
  CLUS_2          36                80
  CLUS_3          17                57
D2V12, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          36                81
  CLUS_2          52               145
  CLUS_3           4                41

Clustering(3) Variable = 2p gain
D3V1, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           0                14
  CLUS_2           3                14
  CLUS_3           2                10
  CLUS_4           1                 9
D3V2, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           1                18
  CLUS_2           2                17
  CLUS_3           3                12
D3V3, multiclass
D3V4, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          19               124
  CLUS_2           7                77
  CLUS_3           8               142
D3V5, multiclass
D3V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN CNV         12    6
  2P GAIN WILD-TYPE  109   67
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          12               109
  CLUS_2           6                67
D3V7, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          19               123
  CLUS_2           8                99
  CLUS_3           9               104
D3V8, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           7                58
  CLUS_2           6                86
  CLUS_3           5                60
  CLUS_4          18               122
D3V9, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          31               176
  CLUS_2          10               134
  CLUS_3           9               123
D3V10, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          14               179
  CLUS_2           7                72
  CLUS_3           4                23
  CLUS_4          25               159
D3V11, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          20               149
  CLUS_2           6               110
  CLUS_3           8                66
D3V12, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           5               112
  CLUS_2          26               171
  CLUS_3           3                42

Clustering(4) Variable = 2q gain
D4V1, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           0                14
  CLUS_2           1                16
  CLUS_3           2                10
  CLUS_4           0                10
D4V2, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           1                18
  CLUS_2           1                18
  CLUS_3           1                14
D4V3, multiclass
D4V4, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          15               128
  CLUS_2           6                78
  CLUS_3           7               143
D4V5, multiclass
D4V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN CNV         10    4
  2Q GAIN WILD-TYPE  111   69
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          10               111
  CLUS_2           4                69
D4V7, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          14               128
  CLUS_2           6               101
  CLUS_3           6               107
D4V8, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           5                60
  CLUS_2           5                87
  CLUS_3           3                62
  CLUS_4          13               127
D4V9, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          26               181
  CLUS_2           7               137
  CLUS_3           7               125
D4V10, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          10               183
  CLUS_2           6                73
  CLUS_3           2                25
  CLUS_4          22               162
D4V11, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          17               152
  CLUS_2           4               112
  CLUS_3           7                67
D4V12, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           4               113
  CLUS_2          22               175
  CLUS_3           2                43

Clustering(5) Variable = 3p gain
D5V1, multiclass
[1] "Remove cluster labels:" "3P GAIN CNV"           
clus
      3P GAIN CNV 3P GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B5-A0JR        TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D5V2, multiclass
[1] "Remove cluster labels:" "3P GAIN CNV"           
clus
      3P GAIN CNV 3P GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B5-A0JR        TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D5V3, multiclass
D5V4, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1          13               130
  CLUS_2           5                79
  CLUS_3           5               145
D5V5, multiclass
D5V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN CNV          4    1
  3P GAIN WILD-TYPE  117   72
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           4               117
  CLUS_2           1                72
D5V7, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1          12               130
  CLUS_2           6               101
  CLUS_3           1               112
D5V8, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0                65
  CLUS_2           3                89
  CLUS_3           5                60
  CLUS_4          11               129
D5V9, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1          16               191
  CLUS_2           6               138
  CLUS_3           6               126
D5V10, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           8               185
  CLUS_2           3                76
  CLUS_3           3                24
  CLUS_4          14               170
D5V11, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1          14               155
  CLUS_2           5               111
  CLUS_3           4                70
D5V12, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           5               112
  CLUS_2          14               183
  CLUS_3           4                41

Clustering(6) Variable = 3q gain
D6V1, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           0                14
  CLUS_2           3                14
  CLUS_3           0                12
  CLUS_4           0                10
D6V2, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           0                19
  CLUS_2           1                18
  CLUS_3           2                13
D6V3, multiclass
D6V4, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          29               114
  CLUS_2           6                78
  CLUS_3           6               144
D6V5, multiclass
D6V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN CNV          4    5
  3Q GAIN WILD-TYPE  117   68
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           4               117
  CLUS_2           5                68
D6V7, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          26               116
  CLUS_2           6               101
  CLUS_3           1               112
D6V8, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           0                65
  CLUS_2           3                89
  CLUS_3           7                58
  CLUS_4          23               117
D6V9, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          37               170
  CLUS_2           7               137
  CLUS_3           6               126
D6V10, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           9               184
  CLUS_2           5                74
  CLUS_3           4                23
  CLUS_4          32               152
D6V11, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          23               146
  CLUS_2           6               110
  CLUS_3          11                63
D6V12, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           6               111
  CLUS_2          30               167
  CLUS_3           4                41

Clustering(7) Variable = 4p gain
D7V1, multiclass
[1] "Remove cluster labels:" "4P GAIN CNV"           
clus
      4P GAIN CNV 4P GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V2, multiclass
[1] "Remove cluster labels:" "4P GAIN CNV"           
clus
      4P GAIN CNV 4P GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V3, multiclass
D7V4, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           2               141
  CLUS_2           2                82
  CLUS_3           0               150
D7V5, multiclass
[1] "Remove cluster labels:" "4P GAIN CNV"           
clus
      4P GAIN CNV 4P GAIN WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G9        TCGA-A5-A0GA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE        TCGA-A5-A0GG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ        TCGA-A5-A0GM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR        TCGA-A5-A0GU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX        TCGA-A5-A0R6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9        TCGA-A5-A0RA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051        TCGA-AP-A052 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A059 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H        TCGA-AP-A05J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P        TCGA-AP-A0LD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG        TCGA-AP-A0LH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL        TCGA-AP-A0LM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT        TCGA-AP-A0LV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L        TCGA-AX-A0IS 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0        TCGA-AX-A0J1 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY        TCGA-B5-A0JZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2        TCGA-B5-A0K3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9        TCGA-B5-A11E 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H        TCGA-B5-A11I 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC        TCGA-BG-A0MG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU        TCGA-BG-A0RY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1        TCGA-BG-A0YU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187        TCGA-BG-A18A 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9        TCGA-BK-A0CA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139        TCGA-BK-A13C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC        TCGA-BS-A0TD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ        TCGA-BS-A0U7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN CNV          0    2
  4P GAIN WILD-TYPE  121   71
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           0               121
  CLUS_2           2                71
D7V7, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           4               138
  CLUS_2           0               107
  CLUS_3           0               113
D7V8, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           0                65
  CLUS_2           0                92
  CLUS_3           0                65
  CLUS_4           4               136
D7V9, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           6               201
  CLUS_2           0               144
  CLUS_3           0               132
D7V10, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           0               193
  CLUS_2           0                79
  CLUS_3           0                27
  CLUS_4           6               178
D7V11, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           3               166
  CLUS_2           0               116
  CLUS_3           1                73
D7V12, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           0               117
  CLUS_2           4               193
  CLUS_3           0                45

Clustering(8) Variable = 5p gain
D8V1, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           0                14
  CLUS_2           2                15
  CLUS_3           1                11
  CLUS_4           0                10
D8V2, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           1                18
  CLUS_2           0                19
  CLUS_3           2                13
D8V3, multiclass
D8V4, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          20               123
  CLUS_2           3                81
  CLUS_3           3               147
D8V5, multiclass
D8V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV          6    2
  5P GAIN WILD-TYPE  115   71
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           6               115
  CLUS_2           2                71
D8V7, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          19               123
  CLUS_2           0               107
  CLUS_3           3               110
D8V8, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           2                63
  CLUS_2           0                92
  CLUS_3           3                62
  CLUS_4          17               123
D8V9, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          25               182
  CLUS_2           1               143
  CLUS_3           5               127
D8V10, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           3               190
  CLUS_2           3                76
  CLUS_3           1                26
  CLUS_4          24               160
D8V11, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          19               150
  CLUS_2           1               115
  CLUS_3           5                69
D8V12, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           0               117
  CLUS_2          22               175
  CLUS_3           3                42

Clustering(9) Variable = 5q gain
D9V1, multiclass
D9V2, multiclass
D9V3, multiclass
D9V4, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           5               138
  CLUS_2           1                83
  CLUS_3           2               148
D9V5, multiclass
[1] "Remove cluster labels:" "5Q GAIN CNV"           
clus
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                1               193 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0        TCGA-AX-A0J1 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY        TCGA-B5-A0JZ 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2        TCGA-B5-A0K3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9        TCGA-B5-A11E 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H        TCGA-B5-A11I 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BS-A0UJ        TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A0ZU        TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A103        TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A15Z        TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A165        TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A16B        TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A16I        TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A16Q        TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A16X        TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A177        TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A17D        TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A17L        TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D1-A17R        TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DI-A0WH 
"5Q GAIN WILD-TYPE" 
D9V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN CNV          1    0
  5Q GAIN WILD-TYPE  120   73
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           1               120
  CLUS_2           0                73
D9V7, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           6               136
  CLUS_2           0               107
  CLUS_3           2               111
D9V8, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           1                64
  CLUS_2           0                92
  CLUS_3           2                63
  CLUS_4           5               135
D9V9, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           7               200
  CLUS_2           0               144
  CLUS_3           2               130
D9V10, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           1               192
  CLUS_2           2                77
  CLUS_3           0                27
  CLUS_4           6               178
D9V11, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           5               164
  CLUS_2           0               116
  CLUS_3           2                72
D9V12, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           0               117
  CLUS_2           7               190
  CLUS_3           0                45

Clustering(10) Variable = 6p gain
D10V1, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           0                14
  CLUS_2           3                14
  CLUS_3           1                11
  CLUS_4           0                10
D10V2, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           0                19
  CLUS_2           1                18
  CLUS_3           3                12
D10V3, multiclass
D10V4, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          19               124
  CLUS_2           7                77
  CLUS_3           7               143
D10V5, multiclass
D10V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV          4    2
  6P GAIN WILD-TYPE  117   71
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           4               117
  CLUS_2           2                71
D10V7, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          16               126
  CLUS_2           5               102
  CLUS_3           2               111
D10V8, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           0                65
  CLUS_2           4                88
  CLUS_3           3                62
  CLUS_4          16               124
D10V9, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          25               182
  CLUS_2           8               136
  CLUS_3           5               127
D10V10, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           9               184
  CLUS_2           4                75
  CLUS_3           2                25
  CLUS_4          23               161
D10V11, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          21               148
  CLUS_2           7               109
  CLUS_3           6                68
D10V12, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           8               109
  CLUS_2          22               175
  CLUS_3           4                41

Clustering(11) Variable = 6q gain
D11V1, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           0                14
  CLUS_2           3                14
  CLUS_3           1                11
  CLUS_4           0                10
D11V2, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           0                19
  CLUS_2           1                18
  CLUS_3           3                12
D11V3, multiclass
D11V4, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1          13               130
  CLUS_2           5                79
  CLUS_3           7               143
D11V5, multiclass
D11V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV          3    2
  6Q GAIN WILD-TYPE  118   71
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           3               118
  CLUS_2           2                71
D11V7, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1          15               127
  CLUS_2           4               103
  CLUS_3           2               111
D11V8, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           0                65
  CLUS_2           3                89
  CLUS_3           3                62
  CLUS_4          15               125
D11V9, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1          18               189
  CLUS_2           7               137
  CLUS_3           5               127
D11V10, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           8               185
  CLUS_2           4                75
  CLUS_3           2                25
  CLUS_4          16               168
D11V11, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1          14               155
  CLUS_2           6               110
  CLUS_3           6                68
D11V12, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           7               110
  CLUS_2          15               182
  CLUS_3           4                41

Clustering(12) Variable = 7p gain
D12V1, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           1                13
  CLUS_2           2                15
  CLUS_3           2                10
  CLUS_4           1                 9
D12V2, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           2                17
  CLUS_2           3                16
  CLUS_3           1                14
D12V3, multiclass
D12V4, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          16               127
  CLUS_2           1                83
  CLUS_3          11               139
D12V5, multiclass
D12V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN CNV         10    2
  7P GAIN WILD-TYPE  111   71
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          10               111
  CLUS_2           2                71
D12V7, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           9               133
  CLUS_2           7               100
  CLUS_3           7               106
D12V8, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           6                59
  CLUS_2           6                86
  CLUS_3           5                60
  CLUS_4           6               134
D12V9, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          21               186
  CLUS_2           8               136
  CLUS_3          14               118
D12V10, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          14               179
  CLUS_2           9                70
  CLUS_3           3                24
  CLUS_4          17               167
D12V11, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          16               153
  CLUS_2           9               107
  CLUS_3           5                69
D12V12, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           7               110
  CLUS_2          18               179
  CLUS_3           5                40

Clustering(13) Variable = 7q gain
D13V1, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           1                13
  CLUS_2           3                14
  CLUS_3           2                10
  CLUS_4           1                 9
D13V2, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           2                17
  CLUS_2           3                16
  CLUS_3           2                13
D13V3, multiclass
D13V4, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          13               130
  CLUS_2           1                83
  CLUS_3          14               136
D13V5, multiclass
D13V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV         10    1
  7Q GAIN WILD-TYPE  111   72
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          10               111
  CLUS_2           1                72
D13V7, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           6               136
  CLUS_2           8                99
  CLUS_3           9               104
D13V8, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           9                56
  CLUS_2           6                86
  CLUS_3           4                61
  CLUS_4           4               136
D13V9, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          18               189
  CLUS_2          10               134
  CLUS_3          15               117
D13V10, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          15               178
  CLUS_2          11                68
  CLUS_3           2                25
  CLUS_4          15               169
D13V11, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          15               154
  CLUS_2          10               106
  CLUS_3           5                69
D13V12, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           9               108
  CLUS_2          16               181
  CLUS_3           5                40

Clustering(14) Variable = 8p gain
D14V1, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                13
  CLUS_2           2                15
  CLUS_3           2                10
  CLUS_4           0                10
D14V2, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                18
  CLUS_2           3                16
  CLUS_3           1                14
D14V3, multiclass
D14V4, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          27               116
  CLUS_2          14                70
  CLUS_3          28               122
D14V5, multiclass
D14V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV         18   11
  8P GAIN WILD-TYPE  103   62
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          18               103
  CLUS_2          11                62
D14V7, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          27               115
  CLUS_2          14                93
  CLUS_3          19                94
D14V8, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          10                55
  CLUS_2          12                80
  CLUS_3           9                56
  CLUS_4          29               111
D14V9, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          40               167
  CLUS_2          20               124
  CLUS_3          25               107
D14V10, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          26               167
  CLUS_2          17                62
  CLUS_3          12                15
  CLUS_4          30               154
D14V11, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          36               133
  CLUS_2          19                97
  CLUS_3          11                63
D14V12, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          15               102
  CLUS_2          35               162
  CLUS_3          16                29

Clustering(15) Variable = 8q gain
D15V1, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           1                13
  CLUS_2           7                10
  CLUS_3           2                10
  CLUS_4           0                10
D15V2, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           1                18
  CLUS_2           3                16
  CLUS_3           6                 9
D15V3, multiclass
D15V4, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          41               102
  CLUS_2          21                63
  CLUS_3          32               118
D15V5, multiclass
D15V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV         25   15
  8Q GAIN WILD-TYPE   96   58
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          25                96
  CLUS_2          15                58
D15V7, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          43                99
  CLUS_2          16                91
  CLUS_3          19                94
D15V8, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          10                55
  CLUS_2          12                80
  CLUS_3           9                56
  CLUS_4          47                93
D15V9, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          66               141
  CLUS_2          25               119
  CLUS_3          24               108
D15V10, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          28               165
  CLUS_2          17                62
  CLUS_3          13                14
  CLUS_4          57               127
D15V11, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          51               118
  CLUS_2          22                94
  CLUS_3          16                58
D15V12, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          18                99
  CLUS_2          52               145
  CLUS_3          19                26

Clustering(16) Variable = 9p gain
D16V1, multiclass
[1] "Remove cluster labels:" "9P GAIN CNV"           
clus
      9P GAIN CNV 9P GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A060        TCGA-AX-A062 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D16V2, multiclass
[1] "Remove cluster labels:" "9P GAIN CNV"           
clus
      9P GAIN CNV 9P GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A060        TCGA-AX-A062 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D16V3, multiclass
D16V4, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           9               134
  CLUS_2           1                83
  CLUS_3           3               147
D16V5, multiclass
[1] "Remove cluster labels:" "9P GAIN CNV"           
clus
      9P GAIN CNV 9P GAIN WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A060        TCGA-AX-A062 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L        TCGA-AX-A0IS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0        TCGA-AX-A0J1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY        TCGA-B5-A0JZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2        TCGA-B5-A0K3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9        TCGA-B5-A11E 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11I        TCGA-B5-A11N 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U        TCGA-B5-A11V 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z        TCGA-B5-A121 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0        TCGA-BG-A0M2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6        TCGA-BG-A0M7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC        TCGA-BG-A0MG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU        TCGA-BG-A0RY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1        TCGA-BG-A0YU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187        TCGA-BG-A18A 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9        TCGA-BK-A0CA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139        TCGA-BK-A13C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC        TCGA-BS-A0TD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ        TCGA-BS-A0U7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D16V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN CNV          1    1
  9P GAIN WILD-TYPE  120   72
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1               120
  CLUS_2           1                72
D16V7, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           4               138
  CLUS_2           2               105
  CLUS_3           2               111
D16V8, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           0                65
  CLUS_2           0                92
  CLUS_3           2                63
  CLUS_4           6               134
D16V9, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1          10               197
  CLUS_2           1               143
  CLUS_3           3               129
D16V10, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2               191
  CLUS_2           1                78
  CLUS_3           0                27
  CLUS_4          11               173
D16V11, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           9               160
  CLUS_2           1               115
  CLUS_3           3                71
D16V12, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1               116
  CLUS_2           9               188
  CLUS_3           3                42

Clustering(17) Variable = 9q gain
D17V1, multiclass
D17V2, multiclass
D17V3, multiclass
D17V4, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           3               140
  CLUS_2           0                84
  CLUS_3           1               149
D17V5, multiclass
D17V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN CNV          0    0
  9Q GAIN WILD-TYPE  121   73
D17V7, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2               140
  CLUS_2           0               107
  CLUS_3           1               112
D17V8, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                65
  CLUS_2           0                92
  CLUS_3           0                65
  CLUS_4           3               137
D17V9, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           3               204
  CLUS_2           0               144
  CLUS_3           1               131
D17V10, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0               193
  CLUS_2           0                79
  CLUS_3           0                27
  CLUS_4           4               180
D17V11, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           3               166
  CLUS_2           0               116
  CLUS_3           1                73
D17V12, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0               117
  CLUS_2           2               195
  CLUS_3           2                43

Clustering(18) Variable = 10p gain
D18V1, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            2                 12
  CLUS_2            2                 15
  CLUS_3            8                  4
  CLUS_4            2                  8
D18V2, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            3                 16
  CLUS_2            9                 10
  CLUS_3            2                 13
D18V3, multiclass
D18V4, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           17                126
  CLUS_2           13                 71
  CLUS_3           30                120
D18V5, multiclass
D18V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN CNV         28   10
  10P GAIN WILD-TYPE   93   63
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           28                 93
  CLUS_2           10                 63
D18V7, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           17                125
  CLUS_2           28                 79
  CLUS_3           19                 94
D18V8, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           15                 50
  CLUS_2           20                 72
  CLUS_3            9                 56
  CLUS_4           20                120
D18V9, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           30                177
  CLUS_2           35                109
  CLUS_3           22                110
D18V10, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           48                145
  CLUS_2           12                 67
  CLUS_3            3                 24
  CLUS_4           24                160
D18V11, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           22                147
  CLUS_2           26                 90
  CLUS_3            8                 66
D18V12, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           27                 90
  CLUS_2           23                174
  CLUS_3            6                 39

Clustering(19) Variable = 10q gain
D19V1, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            1                 13
  CLUS_2            2                 15
  CLUS_3            8                  4
  CLUS_4            2                  8
D19V2, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            2                 17
  CLUS_2            9                 10
  CLUS_3            2                 13
D19V3, multiclass
D19V4, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           15                128
  CLUS_2           11                 73
  CLUS_3           28                122
D19V5, multiclass
D19V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN CNV         25   10
  10Q GAIN WILD-TYPE   96   63
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           25                 96
  CLUS_2           10                 63
D19V7, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           16                126
  CLUS_2           26                 81
  CLUS_3           18                 95
D19V8, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           14                 51
  CLUS_2           19                 73
  CLUS_3            8                 57
  CLUS_4           19                121
D19V9, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           24                183
  CLUS_2           34                110
  CLUS_3           21                111
D19V10, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           46                147
  CLUS_2           12                 67
  CLUS_3            3                 24
  CLUS_4           18                166
D19V11, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           19                150
  CLUS_2           24                 92
  CLUS_3            7                 67
D19V12, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           25                 92
  CLUS_2           21                176
  CLUS_3            4                 41

Clustering(20) Variable = 11p gain
D20V1, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            3                 14
  CLUS_3            0                 12
  CLUS_4            0                 10
D20V2, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            0                 19
  CLUS_2            1                 18
  CLUS_3            2                 13
D20V3, multiclass
D20V4, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            0                143
  CLUS_2            3                 81
  CLUS_3            1                149
D20V5, multiclass
D20V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN CNV          3    1
  11P GAIN WILD-TYPE  118   72
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            3                118
  CLUS_2            1                 72
D20V7, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            4                138
  CLUS_2            1                106
  CLUS_3            0                113
D20V8, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            0                 65
  CLUS_2            1                 91
  CLUS_3            0                 65
  CLUS_4            4                136
D20V9, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            6                201
  CLUS_2            2                142
  CLUS_3            0                132
D20V10, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            2                191
  CLUS_2            0                 79
  CLUS_3            1                 26
  CLUS_4            5                179
D20V11, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            2                167
  CLUS_2            2                114
  CLUS_3            0                 74
D20V12, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            2                115
  CLUS_2            2                195
  CLUS_3            0                 45

Clustering(21) Variable = 11q gain
D21V1, multiclass
[1] "Remove cluster labels:" "11Q GAIN CNV"          
clus
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-BG-A0LW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D21V2, multiclass
[1] "Remove cluster labels:" "11Q GAIN CNV"          
clus
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-BG-A0LW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D21V3, multiclass
D21V4, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            2                141
  CLUS_2            2                 82
  CLUS_3            1                149
D21V5, multiclass
D21V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN CNV          4    0
  11Q GAIN WILD-TYPE  117   73
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            4                117
  CLUS_2            0                 73
D21V7, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            4                138
  CLUS_2            2                105
  CLUS_3            0                113
D21V8, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            0                 65
  CLUS_2            2                 90
  CLUS_3            0                 65
  CLUS_4            4                136
D21V9, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            5                202
  CLUS_2            3                141
  CLUS_3            0                132
D21V10, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            3                190
  CLUS_2            0                 79
  CLUS_3            1                 26
  CLUS_4            4                180
D21V11, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            2                167
  CLUS_2            2                114
  CLUS_3            1                 73
D21V12, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            2                115
  CLUS_2            3                194
  CLUS_3            0                 45

Clustering(22) Variable = 12p gain
D22V1, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            1                 13
  CLUS_2            1                 16
  CLUS_3            2                 10
  CLUS_4            0                 10
D22V2, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            1                 18
  CLUS_2            2                 17
  CLUS_3            1                 14
D22V3, multiclass
D22V4, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           16                127
  CLUS_2            8                 76
  CLUS_3            4                146
D22V5, multiclass
D22V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN CNV          8    4
  12P GAIN WILD-TYPE  113   69
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            8                113
  CLUS_2            4                 69
D22V7, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           15                127
  CLUS_2            7                100
  CLUS_3            3                110
D22V8, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            1                 64
  CLUS_2            6                 86
  CLUS_3            3                 62
  CLUS_4           15                125
D22V9, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           24                183
  CLUS_2            7                137
  CLUS_3            6                126
D22V10, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           11                182
  CLUS_2            3                 76
  CLUS_3            0                 27
  CLUS_4           23                161
D22V11, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           16                153
  CLUS_2            4                112
  CLUS_3            6                 68
D22V12, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            4                113
  CLUS_2           19                178
  CLUS_3            3                 42

Clustering(23) Variable = 12q gain
D23V1, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                 13
  CLUS_2            1                 16
  CLUS_3            2                 10
  CLUS_4            0                 10
D23V2, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                 18
  CLUS_2            2                 17
  CLUS_3            1                 14
D23V3, multiclass
D23V4, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           10                133
  CLUS_2            7                 77
  CLUS_3            4                146
D23V5, multiclass
D23V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN CNV          6    3
  12Q GAIN WILD-TYPE  115   70
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            6                115
  CLUS_2            3                 70
D23V7, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           11                131
  CLUS_2            7                100
  CLUS_3            2                111
D23V8, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                 64
  CLUS_2            6                 86
  CLUS_3            2                 63
  CLUS_4           11                129
D23V9, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           17                190
  CLUS_2            7                137
  CLUS_3            4                128
D23V10, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           10                183
  CLUS_2            3                 76
  CLUS_3            0                 27
  CLUS_4           15                169
D23V11, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           12                157
  CLUS_2            4                112
  CLUS_3            3                 71
D23V12, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            4                113
  CLUS_2           14                183
  CLUS_3            1                 44

Clustering(24) Variable = 13q gain
D24V1, multiclass
[1] "Remove cluster labels:" "13Q GAIN CNV"          
clus
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0LD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D24V2, multiclass
[1] "Remove cluster labels:" "13Q GAIN CNV"          
clus
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0LD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D24V3, multiclass
D24V4, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1           10                133
  CLUS_2            6                 78
  CLUS_3            1                149
D24V5, multiclass
D24V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN CNV          2    3
  13Q GAIN WILD-TYPE  119   70
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            2                119
  CLUS_2            3                 70
D24V7, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1           13                129
  CLUS_2            1                106
  CLUS_3            0                113
D24V8, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            0                 65
  CLUS_2            1                 91
  CLUS_3            0                 65
  CLUS_4           13                127
D24V9, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1           18                189
  CLUS_2            2                142
  CLUS_3            0                132
D24V10, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            2                191
  CLUS_2            0                 79
  CLUS_3            0                 27
  CLUS_4           18                166
D24V11, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            9                160
  CLUS_2            2                114
  CLUS_3            5                 69
D24V12, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            2                115
  CLUS_2           13                184
  CLUS_3            1                 44

Clustering(25) Variable = 14q gain
D25V1, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            1                 13
  CLUS_2            1                 16
  CLUS_3            1                 11
  CLUS_4            0                 10
D25V2, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            1                 18
  CLUS_2            2                 17
  CLUS_3            0                 15
D25V3, multiclass
D25V4, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           10                133
  CLUS_2            3                 81
  CLUS_3            4                146
D25V5, multiclass
D25V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN CNV          3    0
  14Q GAIN WILD-TYPE  118   73
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            3                118
  CLUS_2            0                 73
D25V7, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            5                137
  CLUS_2            3                104
  CLUS_3            1                112
D25V8, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            0                 65
  CLUS_2            2                 90
  CLUS_3            0                 65
  CLUS_4            7                133
D25V9, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           14                193
  CLUS_2            4                140
  CLUS_3            2                130
D25V10, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            4                189
  CLUS_2            1                 78
  CLUS_3            1                 26
  CLUS_4           14                170
D25V11, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           12                157
  CLUS_2            4                112
  CLUS_3            2                 72
D25V12, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            4                113
  CLUS_2           13                184
  CLUS_3            1                 44

Clustering(26) Variable = 15q gain
D26V1, multiclass
D26V2, multiclass
D26V3, multiclass
D26V4, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                142
  CLUS_2            1                 83
  CLUS_3            3                147
D26V5, multiclass
[1] "Remove cluster labels:" "15Q GAIN CNV"          
clus
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 1                193 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GN         TCGA-A5-A0GQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GR         TCGA-A5-A0GU         TCGA-A5-A0GV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0GW         TCGA-A5-A0GX         TCGA-A5-A0R6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0R7         TCGA-A5-A0R8         TCGA-A5-A0R9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-A5-A0RA         TCGA-A5-A0VP         TCGA-A5-A0VQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A059 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A05A         TCGA-AP-A05D         TCGA-AP-A05H 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05O 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0LD         TCGA-AP-A0LE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LF         TCGA-AP-A0LG         TCGA-AP-A0LH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LI         TCGA-AP-A0LJ         TCGA-AP-A0LL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LM         TCGA-AP-A0LN         TCGA-AP-A0LP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06D         TCGA-AX-A06F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A06L         TCGA-AX-A0IS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0IZ         TCGA-AX-A0J0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JN         TCGA-B5-A0JT 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A0JY         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K2         TCGA-B5-A0K3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-B5-A0K7         TCGA-B5-A0K9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11E         TCGA-B5-A11F         TCGA-B5-A11G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11H         TCGA-B5-A11I         TCGA-B5-A11N 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11Q         TCGA-B5-A11S         TCGA-B5-A11U 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11V         TCGA-B5-A11W         TCGA-B5-A11Y 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-B5-A11Z         TCGA-B5-A121         TCGA-BG-A0LW 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0LX         TCGA-BG-A0M0         TCGA-BG-A0M2 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0M3         TCGA-BG-A0M4         TCGA-BG-A0M6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0M7         TCGA-BG-A0M8         TCGA-BG-A0M9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0MC         TCGA-BG-A0MG         TCGA-BG-A0MS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0MT         TCGA-BG-A0MU         TCGA-BG-A0RY 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0VT         TCGA-BG-A0VV         TCGA-BG-A0W1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A0YU         TCGA-BG-A0YV         TCGA-BG-A186 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A187         TCGA-BG-A18A         TCGA-BG-A18B 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BG-A18C         TCGA-BK-A0C9         TCGA-BK-A0CA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BK-A0CB         TCGA-BK-A0CC         TCGA-BK-A139 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BK-A13C         TCGA-BS-A0T9         TCGA-BS-A0TA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0TC         TCGA-BS-A0TD         TCGA-BS-A0TG 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0TI         TCGA-BS-A0TJ         TCGA-BS-A0U7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0U8         TCGA-BS-A0U9         TCGA-BS-A0UF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BS-A0UJ         TCGA-BS-A0V7         TCGA-D1-A0ZP 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZR         TCGA-D1-A0ZU         TCGA-D1-A0ZZ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A101         TCGA-D1-A103         TCGA-D1-A15V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A15W         TCGA-D1-A15X         TCGA-D1-A15Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A160         TCGA-D1-A161         TCGA-D1-A163 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A165         TCGA-D1-A167         TCGA-D1-A168 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A169         TCGA-D1-A16B         TCGA-D1-A16D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16E         TCGA-D1-A16G         TCGA-D1-A16I 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16J         TCGA-D1-A16N         TCGA-D1-A16O 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16Q         TCGA-D1-A16R         TCGA-D1-A16S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A16V         TCGA-D1-A16X         TCGA-D1-A16Y 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A175         TCGA-D1-A176         TCGA-D1-A177 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A179         TCGA-D1-A17B         TCGA-D1-A17C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17D         TCGA-D1-A17F         TCGA-D1-A17H 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17K         TCGA-D1-A17L         TCGA-D1-A17M 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17N         TCGA-D1-A17Q         TCGA-D1-A17R 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D1-A17S         TCGA-D1-A17T         TCGA-D1-A17U 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DI-A0WH 
"15Q GAIN WILD-TYPE" 
D26V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN CNV          1    0
  15Q GAIN WILD-TYPE  120   73
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                120
  CLUS_2            0                 73
D26V7, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                141
  CLUS_2            1                106
  CLUS_3            2                111
D26V8, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                 64
  CLUS_2            0                 92
  CLUS_3            1                 64
  CLUS_4            2                138
D26V9, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            2                205
  CLUS_2            2                142
  CLUS_3            2                130
D26V10, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            3                190
  CLUS_2            1                 78
  CLUS_3            0                 27
  CLUS_4            2                182
D26V11, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                168
  CLUS_2            3                113
  CLUS_3            1                 73
D26V12, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            3                114
  CLUS_2            1                196
  CLUS_3            1                 44

Clustering(27) Variable = 16p gain
D27V1, multiclass
[1] "Remove cluster labels:" "16P GAIN CNV"          
clus
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BK-A0CC 
"16P GAIN WILD-TYPE" 
D27V2, multiclass
[1] "Remove cluster labels:" "16P GAIN CNV"          
clus
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BK-A0CC 
"16P GAIN WILD-TYPE" 
D27V3, multiclass
D27V4, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            8                135
  CLUS_2            0                 84
  CLUS_3            3                147
D27V5, multiclass
D27V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV          3    1
  16P GAIN WILD-TYPE  118   72
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            3                118
  CLUS_2            1                 72
D27V7, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            6                136
  CLUS_2            0                107
  CLUS_3            2                111
D27V8, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            2                 63
  CLUS_2            0                 92
  CLUS_3            0                 65
  CLUS_4            6                134
D27V9, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            9                198
  CLUS_2            1                143
  CLUS_3            2                130
D27V10, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            3                190
  CLUS_2            1                 78
  CLUS_3            0                 27
  CLUS_4            8                176
D27V11, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            5                164
  CLUS_2            2                114
  CLUS_3            3                 71
D27V12, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            2                115
  CLUS_2            8                189
  CLUS_3            0                 45

Clustering(28) Variable = 16q gain
D28V1, multiclass
D28V2, multiclass
D28V3, multiclass
D28V4, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            1                142
  CLUS_2            1                 83
  CLUS_3            2                148
D28V5, multiclass
[1] "Remove cluster labels:" "16Q GAIN CNV"          
clus
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 1                193 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GN         TCGA-A5-A0GQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GR         TCGA-A5-A0GU         TCGA-A5-A0GV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GW         TCGA-A5-A0GX         TCGA-A5-A0R6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0R7         TCGA-A5-A0R8         TCGA-A5-A0R9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0RA         TCGA-A5-A0VP         TCGA-A5-A0VQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A059 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A05A         TCGA-AP-A05D         TCGA-AP-A05H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05O 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0LD         TCGA-AP-A0LE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LF         TCGA-AP-A0LG         TCGA-AP-A0LH 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LI         TCGA-AP-A0LJ         TCGA-AP-A0LL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LM         TCGA-AP-A0LN         TCGA-AP-A0LP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06D         TCGA-AX-A06F 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A06L         TCGA-AX-A0IS 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0IZ         TCGA-AX-A0J0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JN         TCGA-B5-A0JT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0JY         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K2         TCGA-B5-A0K3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-B5-A0K7         TCGA-B5-A0K9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11E         TCGA-B5-A11F         TCGA-B5-A11G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11H         TCGA-B5-A11I         TCGA-B5-A11N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11Q         TCGA-B5-A11S         TCGA-B5-A11U 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11W         TCGA-B5-A11Y         TCGA-B5-A11Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A121         TCGA-BG-A0LW         TCGA-BG-A0LX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0M0         TCGA-BG-A0M2         TCGA-BG-A0M3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0M4         TCGA-BG-A0M6         TCGA-BG-A0M7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0M8         TCGA-BG-A0M9         TCGA-BG-A0MC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0MG         TCGA-BG-A0MS         TCGA-BG-A0MT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0MU         TCGA-BG-A0RY         TCGA-BG-A0VT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0VV         TCGA-BG-A0W1         TCGA-BG-A0YU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC         TCGA-BK-A139         TCGA-BK-A13C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0T9         TCGA-BS-A0TA         TCGA-BS-A0TC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0TD         TCGA-BS-A0TG         TCGA-BS-A0TI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0TJ         TCGA-BS-A0U7         TCGA-BS-A0U8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0U9         TCGA-BS-A0UF         TCGA-BS-A0UJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0V7         TCGA-D1-A0ZP         TCGA-D1-A0ZR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZU         TCGA-D1-A0ZZ         TCGA-D1-A101 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A102         TCGA-D1-A103         TCGA-D1-A15V 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A15W         TCGA-D1-A15X         TCGA-D1-A15Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A160         TCGA-D1-A161         TCGA-D1-A163 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A165         TCGA-D1-A167         TCGA-D1-A168 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A169         TCGA-D1-A16B         TCGA-D1-A16D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16E         TCGA-D1-A16G         TCGA-D1-A16I 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16J         TCGA-D1-A16N         TCGA-D1-A16O 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16Q         TCGA-D1-A16R         TCGA-D1-A16S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16V         TCGA-D1-A16X         TCGA-D1-A16Y 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A175         TCGA-D1-A176         TCGA-D1-A177 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A179         TCGA-D1-A17B         TCGA-D1-A17C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17D         TCGA-D1-A17F         TCGA-D1-A17H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17K         TCGA-D1-A17L         TCGA-D1-A17M 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17N         TCGA-D1-A17Q         TCGA-D1-A17R 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17S         TCGA-D1-A17T         TCGA-D1-A17U 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DI-A0WH 
"16Q GAIN WILD-TYPE" 
D28V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN CNV          1    0
  16Q GAIN WILD-TYPE  120   73
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            1                120
  CLUS_2            0                 73
D28V7, multiclass
[1] "Remove cluster labels:" "16Q GAIN CNV"          
clus
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 2                360 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GN         TCGA-A5-A0GP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GQ         TCGA-A5-A0GR         TCGA-A5-A0GU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GV         TCGA-A5-A0GW         TCGA-A5-A0GX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0R6         TCGA-A5-A0R7         TCGA-A5-A0R8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0R9         TCGA-A5-A0RA         TCGA-A5-A0VP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0VQ         TCGA-A5-A1OF         TCGA-A5-A1OG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A1OJ         TCGA-A5-A1OK         TCGA-AJ-A23M 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AJ-A23O         TCGA-AJ-A2QK         TCGA-AJ-A2QL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AJ-A2QN         TCGA-AP-A051         TCGA-AP-A052 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A053         TCGA-AP-A054         TCGA-AP-A056 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A059         TCGA-AP-A05A         TCGA-AP-A05D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A05O         TCGA-AP-A05P         TCGA-AP-A0L8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LF         TCGA-AP-A0LG         TCGA-AP-A0LH 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LI         TCGA-AP-A0LJ         TCGA-AP-A0LL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LM         TCGA-AP-A0LN         TCGA-AP-A0LO 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LP         TCGA-AP-A0LS         TCGA-AP-A0LT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AP-A1DH         TCGA-AP-A1DK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A1DM         TCGA-AP-A1DO         TCGA-AP-A1DP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A1DQ         TCGA-AP-A1DR         TCGA-AP-A1DV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A1E0         TCGA-AP-A1E1         TCGA-AP-A1E3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A1E4         TCGA-AW-A1PO         TCGA-AX-A05S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05Y 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A06D         TCGA-AX-A06F         TCGA-AX-A06H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A06L         TCGA-AX-A0IS 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A0IU         TCGA-AX-A0IW         TCGA-AX-A0IZ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A0J0         TCGA-AX-A0J1         TCGA-AX-A1C4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1C5         TCGA-AX-A1C7         TCGA-AX-A1C9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1CA         TCGA-AX-A1CC         TCGA-AX-A1CE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1CF         TCGA-AX-A1CI         TCGA-AX-A1CJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1CK         TCGA-AX-A1CN         TCGA-AX-A1CP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1CR         TCGA-AX-A2H2         TCGA-AX-A2H5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A2H7         TCGA-AX-A2H8         TCGA-AX-A2HA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A2HC         TCGA-AX-A2HD         TCGA-AX-A2HF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A2HG         TCGA-AX-A2HJ         TCGA-AX-A2HK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A2IO         TCGA-B5-A0JS         TCGA-B5-A0JT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0JU         TCGA-B5-A0JV         TCGA-B5-A0JX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0JY         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K2         TCGA-B5-A0K3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-B5-A0K6         TCGA-B5-A0K7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0K8         TCGA-B5-A0KB         TCGA-B5-A11E 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11F         TCGA-B5-A11G         TCGA-B5-A11H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11I         TCGA-B5-A11J         TCGA-B5-A11L 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11N         TCGA-B5-A11O         TCGA-B5-A11P 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11Q         TCGA-B5-A11S         TCGA-B5-A11U 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11W         TCGA-B5-A11Y         TCGA-B5-A11Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A121         TCGA-B5-A1MR         TCGA-B5-A1MU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A1MV         TCGA-B5-A1MX         TCGA-B5-A1MY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A1MZ         TCGA-B5-A1N2         TCGA-BG-A0LW 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0LX         TCGA-BG-A0M0         TCGA-BG-A0M2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0M3         TCGA-BG-A0M4         TCGA-BG-A0M6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0M7         TCGA-BG-A0M8         TCGA-BG-A0M9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0MA         TCGA-BG-A0MC         TCGA-BG-A0MG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BG-A0MO         TCGA-BG-A0MQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0MS         TCGA-BG-A0MT         TCGA-BG-A0MU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0RY         TCGA-BG-A0VT         TCGA-BG-A0VV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0VW         TCGA-BG-A0VX         TCGA-BG-A0VZ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0W1         TCGA-BG-A0W2         TCGA-BG-A0YU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A220         TCGA-BG-A221         TCGA-BG-A222 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A2AD         TCGA-BG-A2AE         TCGA-BG-A2L7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC         TCGA-BK-A139         TCGA-BK-A13C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BK-A26L         TCGA-BS-A0T9         TCGA-BS-A0TA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0TC         TCGA-BS-A0TD         TCGA-BS-A0TE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0TG         TCGA-BS-A0TI         TCGA-BS-A0TJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0U5         TCGA-BS-A0U7         TCGA-BS-A0U8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0U9         TCGA-BS-A0UA         TCGA-BS-A0UF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0UJ         TCGA-BS-A0UL         TCGA-BS-A0UT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0UV         TCGA-BS-A0V6         TCGA-BS-A0V8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0VI         TCGA-BS-A0WQ         TCGA-D1-A0ZN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZO         TCGA-D1-A0ZP         TCGA-D1-A0ZQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZR         TCGA-D1-A0ZS         TCGA-D1-A0ZU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZV         TCGA-D1-A0ZZ         TCGA-D1-A101 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A102         TCGA-D1-A103         TCGA-D1-A15V 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A15W         TCGA-D1-A15X         TCGA-D1-A15Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A160         TCGA-D1-A161         TCGA-D1-A163 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A165         TCGA-D1-A167         TCGA-D1-A168 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A169         TCGA-D1-A16B         TCGA-D1-A16D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16E         TCGA-D1-A16G         TCGA-D1-A16I 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16J         TCGA-D1-A16N         TCGA-D1-A16O 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16Q         TCGA-D1-A16R         TCGA-D1-A16S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16V         TCGA-D1-A16X         TCGA-D1-A16Y 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A174         TCGA-D1-A175         TCGA-D1-A176 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A177         TCGA-D1-A179         TCGA-D1-A17A 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17B         TCGA-D1-A17C         TCGA-D1-A17D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17F         TCGA-D1-A17H         TCGA-D1-A17K 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17L         TCGA-D1-A17M         TCGA-D1-A17N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17Q         TCGA-D1-A17R         TCGA-D1-A17S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17T         TCGA-D1-A17U         TCGA-D1-A1NS 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A1NU         TCGA-D1-A1NW         TCGA-D1-A1NX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A1NY         TCGA-D1-A1NZ         TCGA-D1-A1O0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A1O5         TCGA-D1-A1O7         TCGA-D1-A1O8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A2G5         TCGA-D1-A2G6         TCGA-D1-A2G7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DF-A2KS         TCGA-DI-A0WH         TCGA-DI-A1BY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DI-A1NN         TCGA-DI-A1NO         TCGA-DI-A2QU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-E6-A1LX         TCGA-E6-A1LZ         TCGA-E6-A1M0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EC-A1NJ         TCGA-EC-A1QX         TCGA-EC-A24G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EO-A1Y5         TCGA-EO-A1Y8         TCGA-EO-A22R 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EO-A22S         TCGA-EO-A22T         TCGA-EO-A2CG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EO-A2CH         TCGA-EY-A1G7         TCGA-EY-A1G8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GC         TCGA-EY-A1GD         TCGA-EY-A1GE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GF         TCGA-EY-A1GH         TCGA-EY-A1GI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GK         TCGA-EY-A1GM         TCGA-EY-A1GQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GR         TCGA-EY-A1GS         TCGA-EY-A1GT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GU         TCGA-EY-A1GV         TCGA-EY-A1GW 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1H0         TCGA-EY-A212         TCGA-EY-A214 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A215         TCGA-EY-A2OM         TCGA-FI-A2CX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FI-A2CY         TCGA-FI-A2D0         TCGA-FI-A2D2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FI-A2D4         TCGA-FI-A2D5         TCGA-FI-A2D6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FI-A2EU         TCGA-FI-A2EW         TCGA-FI-A2EX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FI-A2F4         TCGA-FI-A2F8         TCGA-FI-A2F9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
D28V8, multiclass
[1] "Remove cluster labels:" "16Q GAIN CNV"          
clus
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 2                360 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GN         TCGA-A5-A0GP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GQ         TCGA-A5-A0GR         TCGA-A5-A0GU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0GV         TCGA-A5-A0GW         TCGA-A5-A0GX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0R6         TCGA-A5-A0R7         TCGA-A5-A0R8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0R9         TCGA-A5-A0RA         TCGA-A5-A0VP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A0VQ         TCGA-A5-A1OF         TCGA-A5-A1OG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-A5-A1OJ         TCGA-A5-A1OK         TCGA-AJ-A23M 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AJ-A23O         TCGA-AJ-A2QK         TCGA-AJ-A2QL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AJ-A2QN         TCGA-AP-A051         TCGA-AP-A052 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A053         TCGA-AP-A054         TCGA-AP-A056 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A059         TCGA-AP-A05A         TCGA-AP-A05D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A05O         TCGA-AP-A05P         TCGA-AP-A0L8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LF         TCGA-AP-A0LG         TCGA-AP-A0LH 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LI         TCGA-AP-A0LJ         TCGA-AP-A0LL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LM         TCGA-AP-A0LN         TCGA-AP-A0LO 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LP         TCGA-AP-A0LS         TCGA-AP-A0LT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AP-A1DH         TCGA-AP-A1DK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A1DM         TCGA-AP-A1DO         TCGA-AP-A1DP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A1DQ         TCGA-AP-A1DR         TCGA-AP-A1DV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A1E0         TCGA-AP-A1E1         TCGA-AP-A1E3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AP-A1E4         TCGA-AW-A1PO         TCGA-AX-A05S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05Y 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A06D         TCGA-AX-A06F         TCGA-AX-A06H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A06L         TCGA-AX-A0IS 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A0IU         TCGA-AX-A0IW         TCGA-AX-A0IZ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A0J0         TCGA-AX-A0J1         TCGA-AX-A1C4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1C5         TCGA-AX-A1C7         TCGA-AX-A1C9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1CA         TCGA-AX-A1CC         TCGA-AX-A1CE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1CF         TCGA-AX-A1CI         TCGA-AX-A1CJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1CK         TCGA-AX-A1CN         TCGA-AX-A1CP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A1CR         TCGA-AX-A2H2         TCGA-AX-A2H5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A2H7         TCGA-AX-A2H8         TCGA-AX-A2HA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A2HC         TCGA-AX-A2HD         TCGA-AX-A2HF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A2HG         TCGA-AX-A2HJ         TCGA-AX-A2HK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AX-A2IO         TCGA-B5-A0JS         TCGA-B5-A0JT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0JU         TCGA-B5-A0JV         TCGA-B5-A0JX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0JY         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K2         TCGA-B5-A0K3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-B5-A0K6         TCGA-B5-A0K7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A0K8         TCGA-B5-A0KB         TCGA-B5-A11E 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11F         TCGA-B5-A11G         TCGA-B5-A11H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11I         TCGA-B5-A11J         TCGA-B5-A11L 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11N         TCGA-B5-A11O         TCGA-B5-A11P 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11Q         TCGA-B5-A11S         TCGA-B5-A11U 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A11W         TCGA-B5-A11Y         TCGA-B5-A11Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A121         TCGA-B5-A1MR         TCGA-B5-A1MU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A1MV         TCGA-B5-A1MX         TCGA-B5-A1MY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B5-A1MZ         TCGA-B5-A1N2         TCGA-BG-A0LW 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0LX         TCGA-BG-A0M0         TCGA-BG-A0M2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0M3         TCGA-BG-A0M4         TCGA-BG-A0M6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0M7         TCGA-BG-A0M8         TCGA-BG-A0M9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0MA         TCGA-BG-A0MC         TCGA-BG-A0MG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BG-A0MO         TCGA-BG-A0MQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0MS         TCGA-BG-A0MT         TCGA-BG-A0MU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0RY         TCGA-BG-A0VT         TCGA-BG-A0VV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0VW         TCGA-BG-A0VX         TCGA-BG-A0VZ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0W1         TCGA-BG-A0W2         TCGA-BG-A0YU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A220         TCGA-BG-A221         TCGA-BG-A222 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BG-A2AD         TCGA-BG-A2AE         TCGA-BG-A2L7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC         TCGA-BK-A139         TCGA-BK-A13C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BK-A26L         TCGA-BS-A0T9         TCGA-BS-A0TA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0TC         TCGA-BS-A0TD         TCGA-BS-A0TE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0TG         TCGA-BS-A0TI         TCGA-BS-A0TJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0U5         TCGA-BS-A0U7         TCGA-BS-A0U8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0U9         TCGA-BS-A0UA         TCGA-BS-A0UF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0UJ         TCGA-BS-A0UL         TCGA-BS-A0UT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0UV         TCGA-BS-A0V6         TCGA-BS-A0V8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BS-A0VI         TCGA-BS-A0WQ         TCGA-D1-A0ZN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZO         TCGA-D1-A0ZP         TCGA-D1-A0ZQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZR         TCGA-D1-A0ZS         TCGA-D1-A0ZU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZV         TCGA-D1-A0ZZ         TCGA-D1-A101 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A102         TCGA-D1-A103         TCGA-D1-A15V 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A15W         TCGA-D1-A15X         TCGA-D1-A15Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A160         TCGA-D1-A161         TCGA-D1-A163 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A165         TCGA-D1-A167         TCGA-D1-A168 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A169         TCGA-D1-A16B         TCGA-D1-A16D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16E         TCGA-D1-A16G         TCGA-D1-A16I 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16J         TCGA-D1-A16N         TCGA-D1-A16O 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16Q         TCGA-D1-A16R         TCGA-D1-A16S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A16V         TCGA-D1-A16X         TCGA-D1-A16Y 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A174         TCGA-D1-A175         TCGA-D1-A176 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A177         TCGA-D1-A179         TCGA-D1-A17A 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17B         TCGA-D1-A17C         TCGA-D1-A17D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17F         TCGA-D1-A17H         TCGA-D1-A17K 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17L         TCGA-D1-A17M         TCGA-D1-A17N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17Q         TCGA-D1-A17R         TCGA-D1-A17S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A17T         TCGA-D1-A17U         TCGA-D1-A1NS 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A1NU         TCGA-D1-A1NW         TCGA-D1-A1NX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A1NY         TCGA-D1-A1NZ         TCGA-D1-A1O0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A1O5         TCGA-D1-A1O7         TCGA-D1-A1O8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D1-A2G5         TCGA-D1-A2G6         TCGA-D1-A2G7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DF-A2KS         TCGA-DI-A0WH         TCGA-DI-A1BY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DI-A1NN         TCGA-DI-A1NO         TCGA-DI-A2QU 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-E6-A1LX         TCGA-E6-A1LZ         TCGA-E6-A1M0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EC-A1NJ         TCGA-EC-A1QX         TCGA-EC-A24G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EO-A1Y5         TCGA-EO-A1Y8         TCGA-EO-A22R 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EO-A22S         TCGA-EO-A22T         TCGA-EO-A2CG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EO-A2CH         TCGA-EY-A1G7         TCGA-EY-A1G8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GC         TCGA-EY-A1GD         TCGA-EY-A1GE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GF         TCGA-EY-A1GH         TCGA-EY-A1GI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GK         TCGA-EY-A1GM         TCGA-EY-A1GQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GR         TCGA-EY-A1GS         TCGA-EY-A1GT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1GU         TCGA-EY-A1GV         TCGA-EY-A1GW 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A1H0         TCGA-EY-A212         TCGA-EY-A214 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EY-A215         TCGA-EY-A2OM         TCGA-FI-A2CX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FI-A2CY         TCGA-FI-A2D0         TCGA-FI-A2D2 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FI-A2D4         TCGA-FI-A2D5         TCGA-FI-A2D6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FI-A2EU         TCGA-FI-A2EW         TCGA-FI-A2EX 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FI-A2F4         TCGA-FI-A2F8         TCGA-FI-A2F9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
D28V9, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            2                205
  CLUS_2            1                143
  CLUS_3            1                131
D28V10, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            2                191
  CLUS_2            1                 78
  CLUS_3            0                 27
  CLUS_4            1                183
D28V11, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            1                168
  CLUS_2            1                115
  CLUS_3            1                 73
D28V12, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            1                116
  CLUS_2            2                195
  CLUS_3            0                 45

Clustering(29) Variable = 17p gain
D29V1, multiclass
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0J1         TCGA-B5-A0JR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-BG-A0LW         TCGA-BG-A0MI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BK-A0C9 
"17P GAIN WILD-TYPE" 
D29V2, multiclass
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0J1         TCGA-B5-A0JR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-BG-A0LW         TCGA-BG-A0MI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BK-A0C9 
"17P GAIN WILD-TYPE" 
D29V3, multiclass
D29V4, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            4                139
  CLUS_2            0                 84
  CLUS_3            1                149
D29V5, multiclass
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 2                192 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GN         TCGA-A5-A0GQ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GR         TCGA-A5-A0GU         TCGA-A5-A0GV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0GW         TCGA-A5-A0GX         TCGA-A5-A0R6 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0R7         TCGA-A5-A0R8         TCGA-A5-A0R9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-A5-A0RA         TCGA-A5-A0VP         TCGA-A5-A0VQ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A059 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05A         TCGA-AP-A05D         TCGA-AP-A05H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05O 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0LD         TCGA-AP-A0LE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LF         TCGA-AP-A0LG         TCGA-AP-A0LH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LI         TCGA-AP-A0LJ         TCGA-AP-A0LL 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LM         TCGA-AP-A0LN         TCGA-AP-A0LP 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06D         TCGA-AX-A06F 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A06L         TCGA-AX-A0IS 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0IZ         TCGA-AX-A0J0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JN         TCGA-B5-A0JT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0JY         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K2         TCGA-B5-A0K3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-B5-A0K7         TCGA-B5-A0K9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A11E         TCGA-B5-A11F         TCGA-B5-A11G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A11H         TCGA-B5-A11I         TCGA-B5-A11N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A11Q         TCGA-B5-A11S         TCGA-B5-A11U 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A11V         TCGA-B5-A11W         TCGA-B5-A11Y 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B5-A11Z         TCGA-B5-A121         TCGA-BG-A0LW 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BG-A0LX         TCGA-BG-A0M0         TCGA-BG-A0M2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BG-A0M3         TCGA-BG-A0M6         TCGA-BG-A0M7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BG-A0M8         TCGA-BG-A0M9         TCGA-BG-A0MC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BG-A0MG         TCGA-BG-A0MS         TCGA-BG-A0MT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BG-A0MU         TCGA-BG-A0RY         TCGA-BG-A0VT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BG-A0VV         TCGA-BG-A0W1         TCGA-BG-A0YU 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BK-A139         TCGA-BK-A13C         TCGA-BS-A0T9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BS-A0TA         TCGA-BS-A0TC         TCGA-BS-A0TD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BS-A0TG         TCGA-BS-A0TI         TCGA-BS-A0TJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BS-A0U7         TCGA-BS-A0U8         TCGA-BS-A0U9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BS-A0UF         TCGA-BS-A0UJ         TCGA-BS-A0V7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A0ZP         TCGA-D1-A0ZR         TCGA-D1-A0ZU 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A0ZZ         TCGA-D1-A101         TCGA-D1-A102 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A103         TCGA-D1-A15V         TCGA-D1-A15W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A15X         TCGA-D1-A15Z         TCGA-D1-A160 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A161         TCGA-D1-A163         TCGA-D1-A165 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A167         TCGA-D1-A168         TCGA-D1-A169 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A16B         TCGA-D1-A16D         TCGA-D1-A16E 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A16G         TCGA-D1-A16I         TCGA-D1-A16J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A16N         TCGA-D1-A16O         TCGA-D1-A16Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A16R         TCGA-D1-A16S         TCGA-D1-A16V 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A16X         TCGA-D1-A16Y         TCGA-D1-A175 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A176         TCGA-D1-A177         TCGA-D1-A179 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A17B         TCGA-D1-A17C         TCGA-D1-A17D 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A17F         TCGA-D1-A17H         TCGA-D1-A17K 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A17L         TCGA-D1-A17M         TCGA-D1-A17N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A17Q         TCGA-D1-A17R         TCGA-D1-A17S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D1-A17T         TCGA-D1-A17U         TCGA-DI-A0WH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D29V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN CNV          1    1
  17P GAIN WILD-TYPE  120   72
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            1                120
  CLUS_2            1                 72
D29V7, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            3                139
  CLUS_2            1                106
  CLUS_3            0                113
D29V8, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            0                 65
  CLUS_2            0                 92
  CLUS_3            2                 63
  CLUS_4            2                138
D29V9, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            6                201
  CLUS_2            0                144
  CLUS_3            1                131
D29V10, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            1                192
  CLUS_2            0                 79
  CLUS_3            0                 27
  CLUS_4            6                178
D29V11, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            3                166
  CLUS_2            1                115
  CLUS_3            1                 73
D29V12, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            1                116
  CLUS_2            4                193
  CLUS_3            0                 45

Clustering(30) Variable = 17q gain
D30V1, multiclass
[1] "Remove cluster labels:" "17Q GAIN CNV"          
clus
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0J1         TCGA-B5-A0JR 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-BG-A0LW         TCGA-BG-A0MI 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9 
"17Q GAIN WILD-TYPE" 
D30V2, multiclass
[1] "Remove cluster labels:" "17Q GAIN CNV"          
clus
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0L9         TCGA-AP-A0LD         TCGA-AP-A0LG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0LH         TCGA-AP-A0LJ         TCGA-AP-A0LN 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AP-A0LT         TCGA-AP-A0LV         TCGA-AX-A05S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A05T         TCGA-AX-A05U         TCGA-AX-A05W 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A05Y         TCGA-AX-A05Z         TCGA-AX-A060 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A062         TCGA-AX-A063         TCGA-AX-A064 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A06B         TCGA-AX-A06F         TCGA-AX-A06J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AX-A0IW         TCGA-AX-A0J1         TCGA-B5-A0JR 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B5-A0K4         TCGA-BG-A0LW         TCGA-BG-A0MI 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9 
"17Q GAIN WILD-TYPE" 
D30V3, multiclass
D30V4, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            9                134
  CLUS_2            0                 84
  CLUS_3            1                149
D30V5, multiclass
D30V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN CNV          3    1
  17Q GAIN WILD-TYPE  118   72
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            3                118
  CLUS_2            1                 72
D30V7, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            7                135
  CLUS_2            2                105
  CLUS_3            0                113
D30V8, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            0                 65
  CLUS_2            1                 91
  CLUS_3            2                 63
  CLUS_4            6                134
D30V9, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           11                196
  CLUS_2            1                143
  CLUS_3            1                131
D30V10, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            2                191
  CLUS_2            0                 79
  CLUS_3            0                 27
  CLUS_4           11                173
D30V11, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            8                161
  CLUS_2            1                115
  CLUS_3            1                 73
D30V12, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            1                116
  CLUS_2            9                188
  CLUS_3            0                 45

Clustering(31) Variable = 18p gain
D31V1, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            1                 13
  CLUS_2            3                 14
  CLUS_3            0                 12
  CLUS_4            0                 10
D31V2, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            1                 18
  CLUS_2            0                 19
  CLUS_3            3                 12
D31V3, multiclass
D31V4, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1           20                123
  CLUS_2            8                 76
  CLUS_3            2                148
D31V5, multiclass
D31V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          3    4
  18P GAIN WILD-TYPE  118   69
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            3                118
  CLUS_2            4                 69
D31V7, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1           18                124
  CLUS_2            2                105
  CLUS_3            1                112
D31V8, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            0                 65
  CLUS_2            1                 91
  CLUS_3            0                 65
  CLUS_4           20                120
D31V9, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1           33                174
  CLUS_2            1                143
  CLUS_3            3                129
D31V10, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                191
  CLUS_2            3                 76
  CLUS_3            0                 27
  CLUS_4           32                152
D31V11, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1           24                145
  CLUS_2            1                115
  CLUS_3            6                 68
D31V12, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                115
  CLUS_2           27                170
  CLUS_3            2                 43

Clustering(32) Variable = 18q gain
D32V1, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            3                 14
  CLUS_3            0                 12
  CLUS_4            0                 10
D32V2, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            0                 19
  CLUS_2            0                 19
  CLUS_3            3                 12
D32V3, multiclass
D32V4, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            8                135
  CLUS_2            7                 77
  CLUS_3            1                149
D32V5, multiclass
[1] "Remove cluster labels:" "18Q GAIN CNV"          
clus
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 2                192 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GN         TCGA-A5-A0GQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A5-A0GR         TCGA-A5-A0GU         TCGA-A5-A0GV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A5-A0GW         TCGA-A5-A0GX         TCGA-A5-A0R6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A5-A0R7         TCGA-A5-A0R8         TCGA-A5-A0R9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A5-A0RA         TCGA-A5-A0VP         TCGA-A5-A0VQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A054 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A059         TCGA-AP-A05A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05O         TCGA-AP-A05P 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LE         TCGA-AP-A0LF 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LL         TCGA-AP-A0LM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LP         TCGA-AP-A0LT 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AX-A06D         TCGA-AX-A06F         TCGA-AX-A06J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AX-A06L         TCGA-AX-A0IS         TCGA-AX-A0IW 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AX-A0IZ         TCGA-AX-A0J0         TCGA-AX-A0J1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A0JN         TCGA-B5-A0JT         TCGA-B5-A0JY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A0K2         TCGA-B5-A0K3         TCGA-B5-A0K4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A0K7         TCGA-B5-A0K9         TCGA-B5-A11E 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A11F         TCGA-B5-A11G         TCGA-B5-A11H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A11I         TCGA-B5-A11N         TCGA-B5-A11Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A11S         TCGA-B5-A11U         TCGA-B5-A11V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A11W         TCGA-B5-A11Y         TCGA-B5-A11Z 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B5-A121         TCGA-BG-A0LW         TCGA-BG-A0LX 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BG-A0M0         TCGA-BG-A0M2         TCGA-BG-A0M3 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BG-A0M4         TCGA-BG-A0M6         TCGA-BG-A0M7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BG-A0M8         TCGA-BG-A0M9         TCGA-BG-A0MC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BG-A0MG         TCGA-BG-A0MS         TCGA-BG-A0MT 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BG-A0MU         TCGA-BG-A0RY         TCGA-BG-A0VT 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BG-A0VV         TCGA-BG-A0W1         TCGA-BG-A0YU 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC         TCGA-BK-A139         TCGA-BK-A13C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BS-A0T9         TCGA-BS-A0TA         TCGA-BS-A0TC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BS-A0TD         TCGA-BS-A0TG         TCGA-BS-A0TI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BS-A0TJ         TCGA-BS-A0U7         TCGA-BS-A0U8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BS-A0U9         TCGA-BS-A0UF         TCGA-BS-A0UJ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BS-A0V7         TCGA-D1-A0ZP         TCGA-D1-A0ZR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZU         TCGA-D1-A0ZZ         TCGA-D1-A101 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A102         TCGA-D1-A103         TCGA-D1-A15V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A15W         TCGA-D1-A15X         TCGA-D1-A15Z 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A160         TCGA-D1-A161         TCGA-D1-A163 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A165         TCGA-D1-A167         TCGA-D1-A168 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A169         TCGA-D1-A16B         TCGA-D1-A16D 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A16E         TCGA-D1-A16G         TCGA-D1-A16J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A16N         TCGA-D1-A16O         TCGA-D1-A16Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A16R         TCGA-D1-A16S         TCGA-D1-A16V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A16X         TCGA-D1-A16Y         TCGA-D1-A175 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A176         TCGA-D1-A177         TCGA-D1-A179 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A17B         TCGA-D1-A17C         TCGA-D1-A17D 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A17F         TCGA-D1-A17H         TCGA-D1-A17K 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A17L         TCGA-D1-A17M         TCGA-D1-A17N 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A17Q         TCGA-D1-A17R         TCGA-D1-A17S 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D1-A17T         TCGA-D1-A17U         TCGA-DI-A0WH 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D32V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          1    1
  18Q GAIN WILD-TYPE  120   72
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                120
  CLUS_2            1                 72
D32V7, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            9                133
  CLUS_2            1                106
  CLUS_3            1                112
D32V8, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            0                 65
  CLUS_2            1                 91
  CLUS_3            0                 65
  CLUS_4           10                130
D32V9, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1           17                190
  CLUS_2            0                144
  CLUS_3            3                129
D32V10, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                192
  CLUS_2            3                 76
  CLUS_3            0                 27
  CLUS_4           16                168
D32V11, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1           14                155
  CLUS_2            0                116
  CLUS_3            3                 71
D32V12, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                116
  CLUS_2           14                183
  CLUS_3            2                 43

Clustering(33) Variable = 19p gain
D33V1, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            4                 13
  CLUS_3            0                 12
  CLUS_4            0                 10
D33V2, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            0                 19
  CLUS_2            0                 19
  CLUS_3            4                 11
D33V3, multiclass
D33V4, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1           16                127
  CLUS_2            7                 77
  CLUS_3            3                147
D33V5, multiclass
D33V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN CNV          1    3
  19P GAIN WILD-TYPE  120   70
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                120
  CLUS_2            3                 70
D33V7, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1           16                126
  CLUS_2            1                106
  CLUS_3            0                113
D33V8, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            0                 65
  CLUS_2            0                 92
  CLUS_3            1                 64
  CLUS_4           16                124
D33V9, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1           27                180
  CLUS_2            3                141
  CLUS_3            1                131
D33V10, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            4                189
  CLUS_2            1                 78
  CLUS_3            2                 25
  CLUS_4           24                160
D33V11, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1           14                155
  CLUS_2            4                112
  CLUS_3            8                 66
D33V12, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            4                113
  CLUS_2           19                178
  CLUS_3            3                 42

Clustering(34) Variable = 19q gain
D34V1, multiclass
[1] "Remove cluster labels:" "19Q GAIN CNV"          
clus
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0J1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D34V2, multiclass
[1] "Remove cluster labels:" "19Q GAIN CNV"          
clus
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0J1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D34V3, multiclass
D34V4, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1           15                128
  CLUS_2            7                 77
  CLUS_3            2                148
D34V5, multiclass
D34V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN CNV          2    1
  19Q GAIN WILD-TYPE  119   72
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            2                119
  CLUS_2            1                 72
D34V7, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1           16                126
  CLUS_2            1                106
  CLUS_3            0                113
D34V8, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            0                 65
  CLUS_2            0                 92
  CLUS_3            0                 65
  CLUS_4           17                123
D34V9, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1           25                182
  CLUS_2            2                142
  CLUS_3            1                131
D34V10, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            3                190
  CLUS_2            1                 78
  CLUS_3            1                 26
  CLUS_4           23                161
D34V11, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1           12                157
  CLUS_2            3                113
  CLUS_3            9                 65
D34V12, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            3                114
  CLUS_2           18                179
  CLUS_3            3                 42

Clustering(35) Variable = 20p gain
D35V1, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            3                 14
  CLUS_3            0                 12
  CLUS_4            0                 10
D35V2, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            0                 19
  CLUS_2            0                 19
  CLUS_3            3                 12
D35V3, multiclass
D35V4, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           37                106
  CLUS_2            9                 75
  CLUS_3           11                139
D35V5, multiclass
D35V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV          8    5
  20P GAIN WILD-TYPE  113   68
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            8                113
  CLUS_2            5                 68
D35V7, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           27                115
  CLUS_2            5                102
  CLUS_3            5                108
D35V8, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            4                 61
  CLUS_2            5                 87
  CLUS_3            4                 61
  CLUS_4           24                116
D35V9, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           50                157
  CLUS_2            7                137
  CLUS_3            8                124
D35V10, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           11                182
  CLUS_2           10                 69
  CLUS_3            0                 27
  CLUS_4           44                140
D35V11, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           35                134
  CLUS_2            8                108
  CLUS_3           12                 62
D35V12, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            7                110
  CLUS_2           42                155
  CLUS_3            6                 39

Clustering(36) Variable = 20q gain
D36V1, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            4                 13
  CLUS_3            0                 12
  CLUS_4            0                 10
D36V2, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            0                 19
  CLUS_2            0                 19
  CLUS_3            4                 11
D36V3, multiclass
D36V4, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           47                 96
  CLUS_2           10                 74
  CLUS_3           12                138
D36V5, multiclass
D36V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV          8    7
  20Q GAIN WILD-TYPE  113   66
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            8                113
  CLUS_2            7                 66
D36V7, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           32                110
  CLUS_2            5                102
  CLUS_3            5                108
D36V8, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            4                 61
  CLUS_2            5                 87
  CLUS_3            4                 61
  CLUS_4           29                111
D36V9, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           61                146
  CLUS_2            8                136
  CLUS_3            8                124
D36V10, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           12                181
  CLUS_2           10                 69
  CLUS_3            0                 27
  CLUS_4           55                129
D36V11, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           45                124
  CLUS_2            9                107
  CLUS_3           13                 61
D36V12, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            8                109
  CLUS_2           52                145
  CLUS_3            7                 38

Clustering(37) Variable = 21q gain
D37V1, multiclass
[1] "Remove cluster labels:" "21Q GAIN CNV"          
clus
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0GA         TCGA-A5-A0GB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0J1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D37V2, multiclass
[1] "Remove cluster labels:" "21Q GAIN CNV"          
clus
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0GA         TCGA-A5-A0GB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0J1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D37V3, multiclass
D37V4, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           12                131
  CLUS_2            6                 78
  CLUS_3            4                146
D37V5, multiclass
D37V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN CNV          1    2
  21Q GAIN WILD-TYPE  120   71
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            1                120
  CLUS_2            2                 71
D37V7, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           12                130
  CLUS_2            1                106
  CLUS_3            0                113
D37V8, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            0                 65
  CLUS_2            1                 91
  CLUS_3            1                 64
  CLUS_4           11                129
D37V9, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           20                187
  CLUS_2            4                140
  CLUS_3            1                131
D37V10, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            4                189
  CLUS_2            1                 78
  CLUS_3            0                 27
  CLUS_4           20                164
D37V11, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           13                156
  CLUS_2            4                112
  CLUS_3            5                 69
D37V12, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            4                113
  CLUS_2           17                180
  CLUS_3            1                 44

Clustering(38) Variable = 22q gain
D38V1, multiclass
[1] "Remove cluster labels:" "22Q GAIN CNV"          
clus
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0GA         TCGA-A5-A0GB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC 
"22Q GAIN WILD-TYPE" 
D38V2, multiclass
[1] "Remove cluster labels:" "22Q GAIN CNV"          
clus
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0GA         TCGA-A5-A0GB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC 
"22Q GAIN WILD-TYPE" 
D38V3, multiclass
D38V4, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            8                135
  CLUS_2            0                 84
  CLUS_3            0                150
D38V5, multiclass
[1] "Remove cluster labels:" "22Q GAIN CNV"          
clus
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 1                193 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GA         TCGA-A5-A0GB         TCGA-A5-A0GD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GG         TCGA-A5-A0GH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GI         TCGA-A5-A0GJ         TCGA-A5-A0GM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GN         TCGA-A5-A0GQ         TCGA-A5-A0GR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GU         TCGA-A5-A0GV         TCGA-A5-A0GW 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0GX         TCGA-A5-A0R6         TCGA-A5-A0R7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0R8         TCGA-A5-A0R9         TCGA-A5-A0RA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-A5-A0VP         TCGA-A5-A0VQ         TCGA-AP-A051 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A059         TCGA-AP-A05A 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05O         TCGA-AP-A05P 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LE         TCGA-AP-A0LF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LL         TCGA-AP-A0LM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LP         TCGA-AP-A0LT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A06D         TCGA-AX-A06F         TCGA-AX-A06J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A06L         TCGA-AX-A0IS         TCGA-AX-A0IW 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AX-A0IZ         TCGA-AX-A0J0         TCGA-AX-A0J1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0JN         TCGA-B5-A0JT         TCGA-B5-A0JY 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0K2         TCGA-B5-A0K3         TCGA-B5-A0K4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A0K7         TCGA-B5-A0K9         TCGA-B5-A11E 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A11F         TCGA-B5-A11G         TCGA-B5-A11H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A11I         TCGA-B5-A11N         TCGA-B5-A11Q 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A11S         TCGA-B5-A11U         TCGA-B5-A11V 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A11W         TCGA-B5-A11Y         TCGA-B5-A11Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B5-A121         TCGA-BG-A0LW         TCGA-BG-A0LX 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0M0         TCGA-BG-A0M2         TCGA-BG-A0M3 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0M4         TCGA-BG-A0M6         TCGA-BG-A0M7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0M8         TCGA-BG-A0M9         TCGA-BG-A0MC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0MG         TCGA-BG-A0MS         TCGA-BG-A0MT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0MU         TCGA-BG-A0RY         TCGA-BG-A0VT 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0VV         TCGA-BG-A0W1         TCGA-BG-A0YU 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BK-A0CC         TCGA-BK-A139         TCGA-BK-A13C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BS-A0T9         TCGA-BS-A0TA         TCGA-BS-A0TC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BS-A0TD         TCGA-BS-A0TG         TCGA-BS-A0TI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BS-A0TJ         TCGA-BS-A0U7         TCGA-BS-A0U8 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BS-A0U9         TCGA-BS-A0UF         TCGA-BS-A0UJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BS-A0V7         TCGA-D1-A0ZP         TCGA-D1-A0ZR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A0ZU         TCGA-D1-A0ZZ         TCGA-D1-A101 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A102         TCGA-D1-A103         TCGA-D1-A15V 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A15W         TCGA-D1-A15X         TCGA-D1-A15Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A160         TCGA-D1-A161         TCGA-D1-A163 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A165         TCGA-D1-A167         TCGA-D1-A168 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A169         TCGA-D1-A16B         TCGA-D1-A16D 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A16E         TCGA-D1-A16G         TCGA-D1-A16I 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A16J         TCGA-D1-A16N         TCGA-D1-A16O 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A16Q         TCGA-D1-A16R         TCGA-D1-A16S 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A16V         TCGA-D1-A16X         TCGA-D1-A16Y 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A175         TCGA-D1-A176         TCGA-D1-A177 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A179         TCGA-D1-A17B         TCGA-D1-A17C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A17D         TCGA-D1-A17F         TCGA-D1-A17H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A17K         TCGA-D1-A17L         TCGA-D1-A17M 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A17N         TCGA-D1-A17Q         TCGA-D1-A17R 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D1-A17S         TCGA-D1-A17T         TCGA-D1-A17U 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DI-A0WH 
"22Q GAIN WILD-TYPE" 
D38V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN CNV          0    1
  22Q GAIN WILD-TYPE  121   72
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            0                121
  CLUS_2            1                 72
D38V7, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            3                139
  CLUS_2            0                107
  CLUS_3            0                113
D38V8, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            0                 65
  CLUS_2            0                 92
  CLUS_3            0                 65
  CLUS_4            3                137
D38V9, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            9                198
  CLUS_2            0                144
  CLUS_3            0                132
D38V10, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            0                193
  CLUS_2            0                 79
  CLUS_3            0                 27
  CLUS_4            9                175
D38V11, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            7                162
  CLUS_2            0                116
  CLUS_3            1                 73
D38V12, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            0                117
  CLUS_2            8                189
  CLUS_3            0                 45

Clustering(39) Variable = Xq gain
D39V1, multiclass
[1] "Remove cluster labels:" "XQ GAIN CNV"           
clus
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D39V2, multiclass
[1] "Remove cluster labels:" "XQ GAIN CNV"           
clus
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D39V3, multiclass
D39V4, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           6               137
  CLUS_2           2                82
  CLUS_3           2               148
D39V5, multiclass
[1] "Remove cluster labels:" "XQ GAIN CNV"           
clus
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                1               193 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A0IS        TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AX-A0J1        TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B5-A0K3        TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B5-A11E        TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B5-A11I        TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B5-A11U        TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B5-A11Z        TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BG-A0M0        TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BS-A0UJ        TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A0ZU        TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A103        TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A15Z        TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A165        TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A16B        TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A16I        TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A16Q        TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A16X        TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A177        TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A17D        TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A17L        TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D1-A17R        TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DI-A0WH 
"XQ GAIN WILD-TYPE" 
D39V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN CNV          0    1
  XQ GAIN WILD-TYPE  121   72
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           0               121
  CLUS_2           1                72
D39V7, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           4               138
  CLUS_2           1               106
  CLUS_3           0               113
D39V8, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           0                65
  CLUS_2           1                91
  CLUS_3           0                65
  CLUS_4           4               136
D39V9, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1          10               197
  CLUS_2           2               142
  CLUS_3           0               132
D39V10, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           3               190
  CLUS_2           0                79
  CLUS_3           0                27
  CLUS_4           9               175
D39V11, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           8               161
  CLUS_2           2               114
  CLUS_3           0                74
D39V12, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           3               114
  CLUS_2           7               190
  CLUS_3           0                45

Clustering(40) Variable = 1p loss
D40V1, multiclass
[1] "Remove cluster labels:" "1P LOSS CNV"           
clus
      1P LOSS CNV 1P LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D40V2, multiclass
[1] "Remove cluster labels:" "1P LOSS CNV"           
clus
      1P LOSS CNV 1P LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP        TCGA-A5-A0GU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D40V3, multiclass
D40V4, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           9               134
  CLUS_2           1                83
  CLUS_3           0               150
D40V5, multiclass
[1] "Remove cluster labels:" "1P LOSS CNV"           
clus
      1P LOSS CNV 1P LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G5        TCGA-A5-A0G9        TCGA-A5-A0GA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE        TCGA-A5-A0GG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ        TCGA-A5-A0GM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0GQ        TCGA-A5-A0GR        TCGA-A5-A0GU        TCGA-A5-A0GV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0GW        TCGA-A5-A0GX        TCGA-A5-A0R6        TCGA-A5-A0R7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0R8        TCGA-A5-A0R9        TCGA-A5-A0RA        TCGA-A5-A0VP 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A5-A0VQ        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A059        TCGA-AP-A05A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A05D        TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A05O        TCGA-AP-A05P        TCGA-AP-A0LD        TCGA-AP-A0LE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LF        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LL        TCGA-AP-A0LM        TCGA-AP-A0LN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AP-A0LP        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06D        TCGA-AX-A06F 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A06L        TCGA-AX-A0IS        TCGA-AX-A0IW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AX-A0IZ        TCGA-AX-A0J0        TCGA-AX-A0J1        TCGA-B5-A0JN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A0JT        TCGA-B5-A0JY        TCGA-B5-A0JZ        TCGA-B5-A0K0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A0K1        TCGA-B5-A0K2        TCGA-B5-A0K3        TCGA-B5-A0K4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A0K7        TCGA-B5-A0K9        TCGA-B5-A11E        TCGA-B5-A11F 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A11G        TCGA-B5-A11H        TCGA-B5-A11I        TCGA-B5-A11N 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U        TCGA-B5-A11V 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z        TCGA-B5-A121 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0        TCGA-BG-A0M2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6        TCGA-BG-A0M7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC        TCGA-BG-A0MG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU        TCGA-BG-A0RY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1        TCGA-BG-A0YU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187        TCGA-BG-A18A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9        TCGA-BK-A0CA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139        TCGA-BK-A13C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC        TCGA-BS-A0TD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ        TCGA-BS-A0U7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D40V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS CNV          1    1
  1P LOSS WILD-TYPE  120   72
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1               120
  CLUS_2           1                72
D40V7, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           6               136
  CLUS_2           0               107
  CLUS_3           1               112
D40V8, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1                64
  CLUS_2           0                92
  CLUS_3           0                65
  CLUS_4           6               134
D40V9, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1          10               197
  CLUS_2           1               143
  CLUS_3           2               130
D40V10, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           0               193
  CLUS_2           2                77
  CLUS_3           1                26
  CLUS_4          10               174
D40V11, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           6               163
  CLUS_2           1               115
  CLUS_3           4                70
D40V12, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1               116
  CLUS_2          10               187
  CLUS_3           0                45

Clustering(41) Variable = 1q loss
D41V1, multiclass
D41V2, multiclass
D41V3, multiclass
D41V4, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           4               139
  CLUS_2           0                84
  CLUS_3           0               150
D41V5, multiclass
D41V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS CNV          0    0
  1Q LOSS WILD-TYPE  121   73
D41V7, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           3               139
  CLUS_2           0               107
  CLUS_3           0               113
D41V8, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0                65
  CLUS_2           0                92
  CLUS_3           0                65
  CLUS_4           3               137
D41V9, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           4               203
  CLUS_2           0               144
  CLUS_3           0               132
D41V10, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0               193
  CLUS_2           0                79
  CLUS_3           0                27
  CLUS_4           4               180
D41V11, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           3               166
  CLUS_2           0               116
  CLUS_3           1                73
D41V12, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0               117
  CLUS_2           4               193
  CLUS_3           0                45

Clustering(42) Variable = 2p loss
D42V1, multiclass
D42V2, multiclass
D42V3, multiclass
D42V4, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           3               140
  CLUS_2           2                82
  CLUS_3           1               149
D42V5, multiclass
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A0IS        TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AX-A0J1        TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A0K3        TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11E        TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11I        TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11U        TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B5-A11Z        TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0M0        TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0M6        TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0MC        TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0MU        TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A0W1        TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BG-A187        TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BK-A0C9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D42V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS CNV          0    2
  2P LOSS WILD-TYPE  121   71
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0               121
  CLUS_2           2                71
D42V7, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           4               138
  CLUS_2           1               106
  CLUS_3           0               113
D42V8, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                65
  CLUS_2           0                92
  CLUS_3           0                65
  CLUS_4           5               135
D42V9, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           3               204
  CLUS_2           1               143
  CLUS_3           2               130
D42V10, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1               192
  CLUS_2           2                77
  CLUS_3           1                26
  CLUS_4           2               182
D42V11, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           3               166
  CLUS_2           1               115
  CLUS_3           1                73
D42V12, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1               116
  CLUS_2           2               195
  CLUS_3           2                43

Clustering(43) Variable = 2q loss
D43V1, multiclass
D43V2, multiclass
D43V3, multiclass
D43V4, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           4               139
  CLUS_2           3                81
  CLUS_3           1               149
D43V5, multiclass
[1] "Remove cluster labels:" "2Q LOSS CNV"           
clus
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05D        TCGA-AP-A05H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LM        TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A06D        TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A0IS        TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AX-A0J1        TCGA-B5-A0JN        TCGA-B5-A0JT        TCGA-B5-A0JY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A0K3        TCGA-B5-A0K4        TCGA-B5-A0K7        TCGA-B5-A0K9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11E        TCGA-B5-A11F        TCGA-B5-A11G        TCGA-B5-A11H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11I        TCGA-B5-A11N        TCGA-B5-A11Q        TCGA-B5-A11S 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11U        TCGA-B5-A11V        TCGA-B5-A11W        TCGA-B5-A11Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-B5-A11Z        TCGA-B5-A121        TCGA-BG-A0LW        TCGA-BG-A0LX 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0M0        TCGA-BG-A0M2        TCGA-BG-A0M3        TCGA-BG-A0M4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0M6        TCGA-BG-A0M7        TCGA-BG-A0M8        TCGA-BG-A0M9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0MC        TCGA-BG-A0MG        TCGA-BG-A0MS        TCGA-BG-A0MT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0MU        TCGA-BG-A0RY        TCGA-BG-A0VT        TCGA-BG-A0VV 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A0W1        TCGA-BG-A0YU        TCGA-BG-A0YV        TCGA-BG-A186 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BG-A187        TCGA-BG-A18A        TCGA-BG-A18B        TCGA-BK-A0C9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BK-A0CA        TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BK-A13C        TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BS-A0TD        TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BS-A0U7        TCGA-BS-A0U8        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D43V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS CNV          0    2
  2Q LOSS WILD-TYPE  121   71
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0               121
  CLUS_2           2                71
D43V7, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           4               138
  CLUS_2           1               106
  CLUS_3           0               113
D43V8, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0                65
  CLUS_2           0                92
  CLUS_3           0                65
  CLUS_4           5               135
D43V9, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           5               202
  CLUS_2           1               143
  CLUS_3           2               130
D43V10, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               192
  CLUS_2           2                77
  CLUS_3           1                26
  CLUS_4           4               180
D43V11, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           4               165
  CLUS_2           1               115
  CLUS_3           2                72
D43V12, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               116
  CLUS_2           4               193
  CLUS_3           2                43

Clustering(44) Variable = 3p loss
D44V1, multiclass
[1] "Remove cluster labels:" "3P LOSS CNV"           
clus
      3P LOSS CNV 3P LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A053        TCGA-AP-A054 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05H        TCGA-AP-A05J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8        TCGA-AP-A0L9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
D44V2, multiclass
[1] "Remove cluster labels:" "3P LOSS CNV"           
clus
      3P LOSS CNV 3P LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A053        TCGA-AP-A054 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05H        TCGA-AP-A05J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8        TCGA-AP-A0L9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
D44V3, multiclass
D44V4, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          19               124
  CLUS_2           6                78
  CLUS_3           2               148
D44V5, multiclass
D44V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          2    7
  3P LOSS WILD-TYPE  119   66
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           2               119
  CLUS_2           7                66
D44V7, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          19               123
  CLUS_2           1               106
  CLUS_3           0               113
D44V8, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                65
  CLUS_2           0                92
  CLUS_3           0                65
  CLUS_4          20               120
D44V9, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          24               183
  CLUS_2           2               142
  CLUS_3           3               129
D44V10, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           2               191
  CLUS_2           3                76
  CLUS_3           1                26
  CLUS_4          23               161
D44V11, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          16               153
  CLUS_2           2               114
  CLUS_3           8                66
D44V12, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           2               115
  CLUS_2          21               176
  CLUS_3           3                42

Clustering(45) Variable = 3q loss
D45V1, multiclass
[1] "Remove cluster labels:" "3Q LOSS CNV"           
clus
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A053        TCGA-AP-A054 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05H        TCGA-AP-A05J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8        TCGA-AP-A0L9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D45V2, multiclass
[1] "Remove cluster labels:" "3Q LOSS CNV"           
clus
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                2                51 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A053        TCGA-AP-A054 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05H        TCGA-AP-A05J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8        TCGA-AP-A0L9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH        TCGA-AP-A0LJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV        TCGA-AX-A05S 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W        TCGA-AX-A05Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062        TCGA-AX-A063 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F        TCGA-AX-A06J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR        TCGA-B5-A0JZ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4        TCGA-BG-A0LW 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D45V3, multiclass
D45V4, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           7               136
  CLUS_2           2                82
  CLUS_3           1               149
D45V5, multiclass
D45V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS CNV          1    2
  3Q LOSS WILD-TYPE  120   71
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           1               120
  CLUS_2           2                71
D45V7, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           8               134
  CLUS_2           1               106
  CLUS_3           0               113
D45V8, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           0                65
  CLUS_2           0                92
  CLUS_3           0                65
  CLUS_4           9               131
D45V9, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           8               199
  CLUS_2           2               142
  CLUS_3           0               132
D45V10, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           2               191
  CLUS_2           0                79
  CLUS_3           0                27
  CLUS_4           8               176
D45V11, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           3               166
  CLUS_2           2               114
  CLUS_3           5                69
D45V12, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           2               115
  CLUS_2           8               189
  CLUS_3           0                45

Clustering(46) Variable = 4p loss
D46V1, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           1                13
  CLUS_2           5                12
  CLUS_3           0                12
  CLUS_4           0                10
D46V2, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           1                18
  CLUS_2           0                19
  CLUS_3           5                10
D46V3, multiclass
D46V4, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          41               102
  CLUS_2          15                69
  CLUS_3           3               147
D46V5, multiclass
D46V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV          7    7
  4P LOSS WILD-TYPE  114   66
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           7               114
  CLUS_2           7                66
D46V7, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          30               112
  CLUS_2           1               106
  CLUS_3           3               110
D46V8, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           2                63
  CLUS_2           1                91
  CLUS_3           2                63
  CLUS_4          29               111
D46V9, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          55               152
  CLUS_2           4               140
  CLUS_3           5               127
D46V10, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           4               189
  CLUS_2           7                72
  CLUS_3           4                23
  CLUS_4          49               135
D46V11, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          39               130
  CLUS_2           6               110
  CLUS_3          14                60
D46V12, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           5               112
  CLUS_2          49               148
  CLUS_3           5                40

Clustering(47) Variable = 4q loss
D47V1, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           1                13
  CLUS_2           2                15
  CLUS_3           0                12
  CLUS_4           0                10
D47V2, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           1                18
  CLUS_2           0                19
  CLUS_3           2                13
D47V3, multiclass
D47V4, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          39               104
  CLUS_2          16                68
  CLUS_3           2               148
D47V5, multiclass
D47V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV          8    6
  4Q LOSS WILD-TYPE  113   67
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           8               113
  CLUS_2           6                67
D47V7, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          27               115
  CLUS_2           0               107
  CLUS_3           5               108
D47V8, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                63
  CLUS_2           0                92
  CLUS_3           2                63
  CLUS_4          28               112
D47V9, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          51               156
  CLUS_2           6               138
  CLUS_3           5               127
D47V10, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           5               188
  CLUS_2           6                73
  CLUS_3           5                22
  CLUS_4          46               138
D47V11, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          37               132
  CLUS_2           6               110
  CLUS_3          14                60
D47V12, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           5               112
  CLUS_2          47               150
  CLUS_3           5                40

Clustering(48) Variable = 5p loss
D48V1, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1                13
  CLUS_2           3                14
  CLUS_3           0                12
  CLUS_4           0                10
D48V2, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1                18
  CLUS_2           0                19
  CLUS_3           3                12
D48V3, multiclass
D48V4, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1          15               128
  CLUS_2           4                80
  CLUS_3           1               149
D48V5, multiclass
D48V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS CNV          4    6
  5P LOSS WILD-TYPE  117   67
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           4               117
  CLUS_2           6                67
D48V7, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1          13               129
  CLUS_2           0               107
  CLUS_3           3               110
D48V8, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0                65
  CLUS_2           0                92
  CLUS_3           3                62
  CLUS_4          13               127
D48V9, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1          22               185
  CLUS_2           3               141
  CLUS_3           2               130
D48V10, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           3               190
  CLUS_2           4                75
  CLUS_3           2                25
  CLUS_4          18               166
D48V11, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1          13               156
  CLUS_2           3               113
  CLUS_3           3                71
D48V12, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2               115
  CLUS_2          15               182
  CLUS_3           2                43

Clustering(49) Variable = 5q loss
D49V1, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           1                13
  CLUS_2           5                12
  CLUS_3           0                12
  CLUS_4           0                10
D49V2, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           1                18
  CLUS_2           0                19
  CLUS_3           5                10
D49V3, multiclass
D49V4, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          29               114
  CLUS_2           6                78
  CLUS_3           1               149
D49V5, multiclass
D49V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS CNV          6    8
  5Q LOSS WILD-TYPE  115   65
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           6               115
  CLUS_2           8                65
D49V7, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          25               117
  CLUS_2           1               106
  CLUS_3           2               111
D49V8, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                65
  CLUS_2           0                92
  CLUS_3           3                62
  CLUS_4          25               115
D49V9, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          38               169
  CLUS_2           4               140
  CLUS_3           2               130
D49V10, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           4               189
  CLUS_2           4                75
  CLUS_3           1                26
  CLUS_4          35               149
D49V11, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          24               145
  CLUS_2           3               113
  CLUS_3           7                67
D49V12, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           3               114
  CLUS_2          30               167
  CLUS_3           1                44

Clustering(50) Variable = 6p loss
D50V1, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1                13
  CLUS_2           2                15
  CLUS_3           0                12
  CLUS_4           0                10
D50V2, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1                18
  CLUS_2           0                19
  CLUS_3           2                13
D50V3, multiclass
D50V4, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           4               139
  CLUS_2           2                82
  CLUS_3           0               150
D50V5, multiclass
D50V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS CNV          1    2
  6P LOSS WILD-TYPE  120   71
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1               120
  CLUS_2           2                71
D50V7, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           4               138
  CLUS_2           0               107
  CLUS_3           1               112
D50V8, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1                64
  CLUS_2           0                92
  CLUS_3           0                65
  CLUS_4           4               136
D50V9, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           7               200
  CLUS_2           1               143
  CLUS_3           1               131
D50V10, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           0               193
  CLUS_2           1                78
  CLUS_3           1                26
  CLUS_4           7               177
D50V11, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           3               166
  CLUS_2           1               115
  CLUS_3           3                71
D50V12, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1               116
  CLUS_2           5               192
  CLUS_3           1                44

Clustering(51) Variable = 6q loss
D51V1, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           1                13
  CLUS_2           2                15
  CLUS_3           0                12
  CLUS_4           0                10
D51V2, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           1                18
  CLUS_2           0                19
  CLUS_3           2                13
D51V3, multiclass
D51V4, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           5               138
  CLUS_2           3                81
  CLUS_3           0               150
D51V5, multiclass
D51V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          1    2
  6Q LOSS WILD-TYPE  120   71
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           1               120
  CLUS_2           2                71
D51V7, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           7               135
  CLUS_2           0               107
  CLUS_3           1               112
D51V8, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           1                64
  CLUS_2           0                92
  CLUS_3           0                65
  CLUS_4           7               133
D51V9, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           8               199
  CLUS_2           1               143
  CLUS_3           2               130
D51V10, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           0               193
  CLUS_2           2                77
  CLUS_3           1                26
  CLUS_4           8               176
D51V11, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           4               165
  CLUS_2           1               115
  CLUS_3           4                70
D51V12, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           1               116
  CLUS_2           6               191
  CLUS_3           2                43

Clustering(52) Variable = 7p loss
D52V1, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           0                14
  CLUS_2           3                14
  CLUS_3           0                12
  CLUS_4           0                10
D52V2, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           0                19
  CLUS_2           0                19
  CLUS_3           3                12
D52V3, multiclass
D52V4, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1          15               128
  CLUS_2           7                77
  CLUS_3           3               147
D52V5, multiclass
D52V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS CNV          2    4
  7P LOSS WILD-TYPE  119   69
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           2               119
  CLUS_2           4                69
D52V7, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1          18               124
  CLUS_2           2               105
  CLUS_3           2               111
D52V8, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           2                63
  CLUS_2           0                92
  CLUS_3           1                64
  CLUS_4          19               121
D52V9, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1          22               185
  CLUS_2           5               139
  CLUS_3           2               130
D52V10, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           4               189
  CLUS_2           4                75
  CLUS_3           1                26
  CLUS_4          20               164
D52V11, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1          13               156
  CLUS_2           4               112
  CLUS_3           7                67
D52V12, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           5               112
  CLUS_2          18               179
  CLUS_3           1                44

Clustering(53) Variable = 7q loss
D53V1, multiclass
[1] "Remove cluster labels:" "7Q LOSS CNV"           
clus
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B5-A0JR        TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
D53V2, multiclass
[1] "Remove cluster labels:" "7Q LOSS CNV"           
clus
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A05H        TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0L8        TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0LH        TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AP-A0LV        TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A05W        TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A062        TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B5-A0JR        TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B5-A0K4        TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
D53V3, multiclass
D53V4, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1          16               127
  CLUS_2           6                78
  CLUS_3           1               149
D53V5, multiclass
D53V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS CNV          1    6
  7Q LOSS WILD-TYPE  120   67
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           1               120
  CLUS_2           6                67
D53V7, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1          17               125
  CLUS_2           0               107
  CLUS_3           0               113
D53V8, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           0                65
  CLUS_2           0                92
  CLUS_3           0                65
  CLUS_4          17               123
D53V9, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1          23               184
  CLUS_2           3               141
  CLUS_3           1               131
D53V10, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           3               190
  CLUS_2           1                78
  CLUS_3           0                27
  CLUS_4          23               161
D53V11, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1          16               153
  CLUS_2           2               114
  CLUS_3           4                70
D53V12, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           3               114
  CLUS_2          19               178
  CLUS_3           0                45

Clustering(54) Variable = 8p loss
D54V1, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           0                14
  CLUS_2           5                12
  CLUS_3           0                12
  CLUS_4           0                10
D54V2, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           0                19
  CLUS_2           0                19
  CLUS_3           5                10
D54V3, multiclass
D54V4, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          36               107
  CLUS_2           9                75
  CLUS_3           1               149
D54V5, multiclass
D54V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV          4    6
  8P LOSS WILD-TYPE  117   67
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           4               117
  CLUS_2           6                67
D54V7, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          30               112
  CLUS_2           0               107
  CLUS_3           1               112
D54V8, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           1                64
  CLUS_2           0                92
  CLUS_3           1                64
  CLUS_4          29               111
D54V9, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          47               160
  CLUS_2           1               143
  CLUS_3           2               130
D54V10, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           1               192
  CLUS_2           2                77
  CLUS_3           0                27
  CLUS_4          47               137
D54V11, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          31               138
  CLUS_2           1               115
  CLUS_3          12                62
D54V12, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           1               116
  CLUS_2          39               158
  CLUS_3           4                41

Clustering(55) Variable = 8q loss
D55V1, multiclass
[1] "Remove cluster labels:" "8Q LOSS CNV"           
clus
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05H 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D55V2, multiclass
[1] "Remove cluster labels:" "8Q LOSS CNV"           
clus
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                1                52 
       TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0GA        TCGA-A5-A0GB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GE        TCGA-A5-A0GH        TCGA-A5-A0GM        TCGA-A5-A0GP 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-AP-A051        TCGA-AP-A052        TCGA-AP-A053 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A054        TCGA-AP-A056        TCGA-AP-A05A        TCGA-AP-A05H 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A05J        TCGA-AP-A05N        TCGA-AP-A05P        TCGA-AP-A0L8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0L9        TCGA-AP-A0LD        TCGA-AP-A0LG        TCGA-AP-A0LH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0LJ        TCGA-AP-A0LN        TCGA-AP-A0LT        TCGA-AP-A0LV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06F 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A06J        TCGA-AX-A0IW        TCGA-AX-A0J1        TCGA-B5-A0JR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A0JZ        TCGA-B5-A0K0        TCGA-B5-A0K1        TCGA-B5-A0K4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0MI        TCGA-BK-A0C9        TCGA-BK-A0CC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D55V3, multiclass
D55V4, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           9               134
  CLUS_2           1                83
  CLUS_3           0               150
D55V5, multiclass
[1] "Remove cluster labels:" "8Q LOSS CNV"           
clus
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                2               192 
       TCGA-A5-A0G1        TCGA-A5-A0G2        TCGA-A5-A0G5        TCGA-A5-A0G9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GA        TCGA-A5-A0GB        TCGA-A5-A0GD        TCGA-A5-A0GE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GG        TCGA-A5-A0GH        TCGA-A5-A0GI        TCGA-A5-A0GJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GM        TCGA-A5-A0GN        TCGA-A5-A0GQ        TCGA-A5-A0GR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0GU        TCGA-A5-A0GV        TCGA-A5-A0GW        TCGA-A5-A0GX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0R6        TCGA-A5-A0R7        TCGA-A5-A0R8        TCGA-A5-A0R9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A5-A0RA        TCGA-A5-A0VP        TCGA-A5-A0VQ        TCGA-AP-A051 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A052        TCGA-AP-A053        TCGA-AP-A054        TCGA-AP-A056 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A059        TCGA-AP-A05A        TCGA-AP-A05H        TCGA-AP-A05J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A05N        TCGA-AP-A05O        TCGA-AP-A05P        TCGA-AP-A0LD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0LE        TCGA-AP-A0LF        TCGA-AP-A0LG        TCGA-AP-A0LH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0LI        TCGA-AP-A0LJ        TCGA-AP-A0LL        TCGA-AP-A0LM 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AP-A0LN        TCGA-AP-A0LP        TCGA-AP-A0LT        TCGA-AP-A0LV 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05S        TCGA-AX-A05T        TCGA-AX-A05U        TCGA-AX-A05W 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A05Y        TCGA-AX-A05Z        TCGA-AX-A060        TCGA-AX-A062 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A063        TCGA-AX-A064        TCGA-AX-A06B        TCGA-AX-A06D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A06F        TCGA-AX-A06J        TCGA-AX-A06L        TCGA-AX-A0IS 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AX-A0IW        TCGA-AX-A0IZ        TCGA-AX-A0J0        TCGA-AX-A0J1 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A0JT        TCGA-B5-A0JY        TCGA-B5-A0JZ        TCGA-B5-A0K0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A0K1        TCGA-B5-A0K2        TCGA-B5-A0K3        TCGA-B5-A0K4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A0K7        TCGA-B5-A0K9        TCGA-B5-A11E        TCGA-B5-A11F 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A11G        TCGA-B5-A11H        TCGA-B5-A11I        TCGA-B5-A11N 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A11Q        TCGA-B5-A11S        TCGA-B5-A11U        TCGA-B5-A11V 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B5-A11W        TCGA-B5-A11Y        TCGA-B5-A11Z        TCGA-B5-A121 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0LW        TCGA-BG-A0LX        TCGA-BG-A0M0        TCGA-BG-A0M2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0M3        TCGA-BG-A0M4        TCGA-BG-A0M6        TCGA-BG-A0M7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0M8        TCGA-BG-A0M9        TCGA-BG-A0MC        TCGA-BG-A0MG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0MS        TCGA-BG-A0MT        TCGA-BG-A0MU        TCGA-BG-A0RY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0VT        TCGA-BG-A0VV        TCGA-BG-A0W1        TCGA-BG-A0YU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A0YV        TCGA-BG-A186        TCGA-BG-A187        TCGA-BG-A18A 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BG-A18B        TCGA-BG-A18C        TCGA-BK-A0C9        TCGA-BK-A0CA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BK-A0CB        TCGA-BK-A0CC        TCGA-BK-A139        TCGA-BK-A13C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BS-A0T9        TCGA-BS-A0TA        TCGA-BS-A0TC        TCGA-BS-A0TD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BS-A0TG        TCGA-BS-A0TI        TCGA-BS-A0TJ        TCGA-BS-A0U7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BS-A0U8        TCGA-BS-A0U9        TCGA-BS-A0UF        TCGA-BS-A0UJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BS-A0V7        TCGA-D1-A0ZP        TCGA-D1-A0ZR        TCGA-D1-A0ZU 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A0ZZ        TCGA-D1-A101        TCGA-D1-A102        TCGA-D1-A103 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A15V        TCGA-D1-A15W        TCGA-D1-A15X        TCGA-D1-A15Z 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A160        TCGA-D1-A161        TCGA-D1-A163        TCGA-D1-A165 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A167        TCGA-D1-A168        TCGA-D1-A169        TCGA-D1-A16B 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A16D        TCGA-D1-A16E        TCGA-D1-A16G        TCGA-D1-A16I 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A16J        TCGA-D1-A16N        TCGA-D1-A16O        TCGA-D1-A16Q 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A16R        TCGA-D1-A16S        TCGA-D1-A16V        TCGA-D1-A16X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A16Y        TCGA-D1-A175        TCGA-D1-A176        TCGA-D1-A177 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A179        TCGA-D1-A17B        TCGA-D1-A17C        TCGA-D1-A17D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A17F        TCGA-D1-A17H        TCGA-D1-A17K        TCGA-D1-A17L 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A17M        TCGA-D1-A17N        TCGA-D1-A17Q        TCGA-D1-A17R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D1-A17S        TCGA-D1-A17T        TCGA-D1-A17U        TCGA-DI-A0WH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D55V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS CNV          1    1
  8Q LOSS WILD-TYPE  120   72
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           1               120
  CLUS_2           1                72
D55V7, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           4               138
  CLUS_2           0               107
  CLUS_3           0               113
D55V8, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           0                65
  CLUS_2           0                92
  CLUS_3           0                65
  CLUS_4           4               136
D55V9, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1          11               196
  CLUS_2           0               144
  CLUS_3           0               132
D55V10, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           0               193
  CLUS_2           0                79
  CLUS_3           0                27
  CLUS_4          11               173
D55V11, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1          10               159
  CLUS_2           0               116
  CLUS_3           0                74
D55V12, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           0               117
  CLUS_2          10               187
  CLUS_3           0                45

Clustering(56) Variable = 9p loss
D56V1, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           1                13
  CLUS_2           6                11
  CLUS_3           0                12
  CLUS_4           0                10
D56V2, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           1                18
  CLUS_2           0                19
  CLUS_3           6                 9
D56V3, multiclass
D56V4, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          36               107
  CLUS_2          19                65
  CLUS_3           8               142
D56V5, multiclass
D56V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV         11   11
  9P LOSS WILD-TYPE  110   62
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          11               110
  CLUS_2          11                62
D56V7, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          41               101
  CLUS_2           3               104
  CLUS_3           3               110
D56V8, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           0                65
  CLUS_2           1                91
  CLUS_3           3                62
  CLUS_4          43                97
D56V9, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          55               152
  CLUS_2          15               129
  CLUS_3           4               128
D56V10, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          14               179
  CLUS_2           4                75
  CLUS_3           4                23
  CLUS_4          52               132
D56V11, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          38               131
  CLUS_2          12               104
  CLUS_3          12                62
D56V12, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          12               105
  CLUS_2          45               152
  CLUS_3           5                40

Clustering(57) Variable = 9q loss
D57V1, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           0                14
  CLUS_2           7                10
  CLUS_3           0                12
  CLUS_4           0                10
D57V2, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           0                19
  CLUS_2           0                19
  CLUS_3           7                 8
D57V3, multiclass
D57V4, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          46                97
  CLUS_2          21                63
  CLUS_3          12               138
D57V5, multiclass
D57V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS CNV         13   11
  9Q LOSS WILD-TYPE  108   62
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          13               108
  CLUS_2          11                62
D57V7, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          48                94
  CLUS_2           4               103
  CLUS_3           5               108
D57V8, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           0                65
  CLUS_2           2                90
  CLUS_3           5                60
  CLUS_4          50                90
D57V9, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          69               138
  CLUS_2          16               128
  CLUS_3           6               126
D57V10, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          15               178
  CLUS_2           8                71
  CLUS_3           6                21
  CLUS_4          62               122
D57V11, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          46               123
  CLUS_2          14               102
  CLUS_3          18                56
D57V12, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          14               103
  CLUS_2          54               143
  CLUS_3          10                35

Clustering(58) Variable = 10p loss
D58V1, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            3                 14
  CLUS_3            0                 12
  CLUS_4            0                 10
D58V2, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            0                 19
  CLUS_2            0                 19
  CLUS_3            3                 12
D58V3, multiclass
D58V4, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           15                128
  CLUS_2            4                 80
  CLUS_3            1                149
D58V5, multiclass
D58V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          2    2
  10P LOSS WILD-TYPE  119   71
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            2                119
  CLUS_2            2                 71
D58V7, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           11                131
  CLUS_2            1                106
  CLUS_3            0                113
D58V8, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            0                 65
  CLUS_2            0                 92
  CLUS_3            1                 64
  CLUS_4           11                129
D58V9, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           20                187
  CLUS_2            1                143
  CLUS_3            1                131
D58V10, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            2                191
  CLUS_2            2                 77
  CLUS_3            1                 26
  CLUS_4           17                167
D58V11, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           11                158
  CLUS_2            2                114
  CLUS_3            6                 68
D58V12, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            2                115
  CLUS_2           16                181
  CLUS_3            1                 44

Clustering(59) Variable = 10q loss
D59V1, multiclass
[1] "Remove cluster labels:" "10Q LOSS CNV"          
clus
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06F 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
D59V2, multiclass
[1] "Remove cluster labels:" "10Q LOSS CNV"          
clus
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05P         TCGA-AP-A0L8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06F 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
D59V3, multiclass
D59V4, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           16                127
  CLUS_2            5                 79
  CLUS_3            1                149
D59V5, multiclass
D59V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          3    2
  10Q LOSS WILD-TYPE  118   71
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            3                118
  CLUS_2            2                 71
D59V7, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           11                131
  CLUS_2            1                106
  CLUS_3            0                113
D59V8, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            0                 65
  CLUS_2            0                 92
  CLUS_3            2                 63
  CLUS_4           10                130
D59V9, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           20                187
  CLUS_2            2                142
  CLUS_3            2                130
D59V10, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            3                190
  CLUS_2            2                 77
  CLUS_3            1                 26
  CLUS_4           18                166
D59V11, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           14                155
  CLUS_2            3                113
  CLUS_3            4                 70
D59V12, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            3                114
  CLUS_2           16                181
  CLUS_3            2                 43

Clustering(60) Variable = 11p loss
D60V1, multiclass
[1] "Remove cluster labels:" "11P LOSS CNV"          
clus
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05D 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06F 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D60V2, multiclass
[1] "Remove cluster labels:" "11P LOSS CNV"          
clus
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05D 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A05H         TCGA-AP-A05J         TCGA-AP-A05N 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06F 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D60V3, multiclass
D60V4, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           30                113
  CLUS_2           14                 70
  CLUS_3            4                146
D60V5, multiclass
D60V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV          6    5
  11P LOSS WILD-TYPE  115   68
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            6                115
  CLUS_2            5                 68
D60V7, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           24                118
  CLUS_2            0                107
  CLUS_3            3                110
D60V8, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                 64
  CLUS_2            0                 92
  CLUS_3            2                 63
  CLUS_4           24                116
D60V9, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           42                165
  CLUS_2            7                137
  CLUS_3            3                129
D60V10, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            7                186
  CLUS_2            5                 74
  CLUS_3            3                 24
  CLUS_4           37                147
D60V11, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           32                137
  CLUS_2            7                109
  CLUS_3            9                 65
D60V12, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            7                110
  CLUS_2           37                160
  CLUS_3            4                 41

Clustering(61) Variable = 11q loss
D61V1, multiclass
D61V2, multiclass
D61V3, multiclass
D61V4, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1           26                117
  CLUS_2           12                 72
  CLUS_3            5                145
D61V5, multiclass
D61V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV          5    2
  11Q LOSS WILD-TYPE  116   71
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            5                116
  CLUS_2            2                 71
D61V7, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1           17                125
  CLUS_2            2                105
  CLUS_3            2                111
D61V8, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                 64
  CLUS_2            0                 92
  CLUS_3            1                 64
  CLUS_4           19                121
D61V9, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1           35                172
  CLUS_2            7                137
  CLUS_3            3                129
D61V10, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            8                185
  CLUS_2            4                 75
  CLUS_3            2                 25
  CLUS_4           31                153
D61V11, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1           29                140
  CLUS_2            8                108
  CLUS_3            6                 68
D61V12, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            8                109
  CLUS_2           32                165
  CLUS_3            3                 42

Clustering(62) Variable = 12p loss
D62V1, multiclass
[1] "Remove cluster labels:" "12P LOSS CNV"          
clus
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06F 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D62V2, multiclass
[1] "Remove cluster labels:" "12P LOSS CNV"          
clus
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06F 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D62V3, multiclass
D62V4, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           16                127
  CLUS_2            5                 79
  CLUS_3            1                149
D62V5, multiclass
D62V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS CNV          4    3
  12P LOSS WILD-TYPE  117   70
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            4                117
  CLUS_2            3                 70
D62V7, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           12                130
  CLUS_2            0                107
  CLUS_3            0                113
D62V8, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            0                 65
  CLUS_2            0                 92
  CLUS_3            2                 63
  CLUS_4           10                130
D62V9, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           23                184
  CLUS_2            1                143
  CLUS_3            0                132
D62V10, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                192
  CLUS_2            1                 78
  CLUS_3            1                 26
  CLUS_4           21                163
D62V11, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           15                154
  CLUS_2            1                115
  CLUS_3            5                 69
D62V12, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                116
  CLUS_2           20                177
  CLUS_3            0                 45

Clustering(63) Variable = 12q loss
D63V1, multiclass
[1] "Remove cluster labels:" "12Q LOSS CNV"          
clus
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BK-A0CC 
"12Q LOSS WILD-TYPE" 
D63V2, multiclass
[1] "Remove cluster labels:" "12Q LOSS CNV"          
clus
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BK-A0CC 
"12Q LOSS WILD-TYPE" 
D63V3, multiclass
D63V4, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1           13                130
  CLUS_2            3                 81
  CLUS_3            0                150
D63V5, multiclass
D63V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS CNV          3    4
  12Q LOSS WILD-TYPE  118   69
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            3                118
  CLUS_2            4                 69
D63V7, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            8                134
  CLUS_2            0                107
  CLUS_3            0                113
D63V8, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            0                 65
  CLUS_2            0                 92
  CLUS_3            0                 65
  CLUS_4            8                132
D63V9, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1           17                190
  CLUS_2            0                144
  CLUS_3            0                132
D63V10, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            0                193
  CLUS_2            0                 79
  CLUS_3            0                 27
  CLUS_4           17                167
D63V11, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1           11                158
  CLUS_2            0                116
  CLUS_3            4                 70
D63V12, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            0                117
  CLUS_2           15                182
  CLUS_3            0                 45

Clustering(64) Variable = 13q loss
D64V1, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            1                 13
  CLUS_2            2                 15
  CLUS_3            0                 12
  CLUS_4            0                 10
D64V2, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            1                 18
  CLUS_2            0                 19
  CLUS_3            2                 13
D64V3, multiclass
D64V4, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           31                112
  CLUS_2           14                 70
  CLUS_3            8                142
D64V5, multiclass
D64V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          7    7
  13Q LOSS WILD-TYPE  114   66
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            7                114
  CLUS_2            7                 66
D64V7, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           23                119
  CLUS_2            3                104
  CLUS_3            6                107
D64V8, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            3                 62
  CLUS_2            1                 91
  CLUS_3            2                 63
  CLUS_4           26                114
D64V9, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           41                166
  CLUS_2           10                134
  CLUS_3            8                124
D64V10, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           11                182
  CLUS_2            7                 72
  CLUS_3            6                 21
  CLUS_4           35                149
D64V11, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           31                138
  CLUS_2           13                103
  CLUS_3            9                 65
D64V12, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           10                107
  CLUS_2           36                161
  CLUS_3            7                 38

Clustering(65) Variable = 14q loss
D65V1, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            5                 12
  CLUS_3            0                 12
  CLUS_4            0                 10
D65V2, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            0                 19
  CLUS_2            0                 19
  CLUS_3            5                 10
D65V3, multiclass
D65V4, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           27                116
  CLUS_2            5                 79
  CLUS_3            0                150
D65V5, multiclass
D65V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS CNV          3   10
  14Q LOSS WILD-TYPE  118   63
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            3                118
  CLUS_2           10                 63
D65V7, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           23                119
  CLUS_2            0                107
  CLUS_3            2                111
D65V8, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            1                 64
  CLUS_2            0                 92
  CLUS_3            1                 64
  CLUS_4           23                117
D65V9, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           35                172
  CLUS_2            1                143
  CLUS_3            4                128
D65V10, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            0                193
  CLUS_2            4                 75
  CLUS_3            1                 26
  CLUS_4           35                149
D65V11, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           26                143
  CLUS_2            1                115
  CLUS_3            5                 69
D65V12, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            1                116
  CLUS_2           28                169
  CLUS_3            3                 42

Clustering(66) Variable = 15q loss
D66V1, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            6                 11
  CLUS_3            0                 12
  CLUS_4            0                 10
D66V2, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            0                 19
  CLUS_2            0                 19
  CLUS_3            6                  9
D66V3, multiclass
D66V4, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           50                 93
  CLUS_2           17                 67
  CLUS_3            4                146
D66V5, multiclass
D66V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS CNV          7    8
  15Q LOSS WILD-TYPE  114   65
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            7                114
  CLUS_2            8                 65
D66V7, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           36                106
  CLUS_2            2                105
  CLUS_3            5                108
D66V8, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            1                 64
  CLUS_2            1                 91
  CLUS_3            4                 61
  CLUS_4           37                103
D66V9, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           66                141
  CLUS_2            7                137
  CLUS_3            6                126
D66V10, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            4                189
  CLUS_2            8                 71
  CLUS_3            6                 21
  CLUS_4           61                123
D66V11, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           48                121
  CLUS_2            6                110
  CLUS_3           16                 58
D66V12, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            5                112
  CLUS_2           58                139
  CLUS_3            7                 38

Clustering(67) Variable = 16p loss
D67V1, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            5                 12
  CLUS_3            0                 12
  CLUS_4            0                 10
D67V2, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            0                 19
  CLUS_2            0                 19
  CLUS_3            5                 10
D67V3, multiclass
D67V4, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1           38                105
  CLUS_2           17                 67
  CLUS_3            4                146
D67V5, multiclass
D67V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS CNV         10    7
  16P LOSS WILD-TYPE  111   66
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1           10                111
  CLUS_2            7                 66
D67V7, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1           35                107
  CLUS_2            2                105
  CLUS_3            4                109
D67V8, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            3                 62
  CLUS_2            1                 91
  CLUS_3            2                 63
  CLUS_4           35                105
D67V9, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1           52                155
  CLUS_2            6                138
  CLUS_3            8                124
D67V10, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            6                187
  CLUS_2            7                 72
  CLUS_3            4                 23
  CLUS_4           49                135
D67V11, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1           38                131
  CLUS_2            5                111
  CLUS_3           15                 59
D67V12, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            6                111
  CLUS_2           47                150
  CLUS_3            5                 40

Clustering(68) Variable = 16q loss
D68V1, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            7                 10
  CLUS_3            1                 11
  CLUS_4            0                 10
D68V2, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            0                 19
  CLUS_2            1                 18
  CLUS_3            7                  8
D68V3, multiclass
D68V4, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           58                 85
  CLUS_2           25                 59
  CLUS_3           11                139
D68V5, multiclass
D68V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS CNV         18   10
  16Q LOSS WILD-TYPE  103   63
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           18                103
  CLUS_2           10                 63
D68V7, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           54                 88
  CLUS_2            6                101
  CLUS_3           11                102
D68V8, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            9                 56
  CLUS_2            4                 88
  CLUS_3            6                 59
  CLUS_4           52                 88
D68V9, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           77                130
  CLUS_2           12                132
  CLUS_3           17                115
D68V10, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           18                175
  CLUS_2           11                 68
  CLUS_3            5                 22
  CLUS_4           72                112
D68V11, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           59                110
  CLUS_2           12                104
  CLUS_3           21                 53
D68V12, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           13                104
  CLUS_2           69                128
  CLUS_3           10                 35

Clustering(69) Variable = 17p loss
D69V1, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            7                 10
  CLUS_3            1                 11
  CLUS_4            0                 10
D69V2, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            1                 18
  CLUS_2            0                 19
  CLUS_3            7                  8
D69V3, multiclass
D69V4, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           61                 82
  CLUS_2           18                 66
  CLUS_3           10                140
D69V5, multiclass
D69V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV         15   11
  17P LOSS WILD-TYPE  106   62
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           15                106
  CLUS_2           11                 62
D69V7, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           58                 84
  CLUS_2            2                105
  CLUS_3            4                109
D69V8, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            1                 64
  CLUS_2            0                 92
  CLUS_3            5                 60
  CLUS_4           58                 82
D69V9, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           81                126
  CLUS_2           15                129
  CLUS_3            6                126
D69V10, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           15                178
  CLUS_2            7                 72
  CLUS_3            5                 22
  CLUS_4           75                109
D69V11, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           56                113
  CLUS_2           12                104
  CLUS_3           19                 55
D69V12, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           12                105
  CLUS_2           64                133
  CLUS_3           11                 34

Clustering(70) Variable = 17q loss
D70V1, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            5                 12
  CLUS_3            0                 12
  CLUS_4            0                 10
D70V2, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            0                 19
  CLUS_2            0                 19
  CLUS_3            5                 10
D70V3, multiclass
D70V4, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1           35                108
  CLUS_2           14                 70
  CLUS_3            9                141
D70V5, multiclass
D70V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS CNV         10    8
  17Q LOSS WILD-TYPE  111   65
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1           10                111
  CLUS_2            8                 65
D70V7, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1           33                109
  CLUS_2            2                105
  CLUS_3            4                109
D70V8, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            1                 64
  CLUS_2            0                 92
  CLUS_3            3                 62
  CLUS_4           35                105
D70V9, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1           48                159
  CLUS_2           11                133
  CLUS_3            6                126
D70V10, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1           11                182
  CLUS_2            5                 74
  CLUS_3            5                 22
  CLUS_4           44                140
D70V11, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1           37                132
  CLUS_2            9                107
  CLUS_3           11                 63
D70V12, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            8                109
  CLUS_2           38                159
  CLUS_3           11                 34

Clustering(71) Variable = 18p loss
D71V1, multiclass
[1] "Remove cluster labels:" "18P LOSS CNV"          
clus
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
D71V2, multiclass
[1] "Remove cluster labels:" "18P LOSS CNV"          
clus
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LJ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
D71V3, multiclass
D71V4, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           22                121
  CLUS_2            6                 78
  CLUS_3            2                148
D71V5, multiclass
D71V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV          7    3
  18P LOSS WILD-TYPE  114   70
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            7                114
  CLUS_2            3                 70
D71V7, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           17                125
  CLUS_2            1                106
  CLUS_3            4                109
D71V8, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            1                 64
  CLUS_2            0                 92
  CLUS_3            4                 61
  CLUS_4           17                123
D71V9, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           24                183
  CLUS_2            4                140
  CLUS_3            7                125
D71V10, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            4                189
  CLUS_2            6                 73
  CLUS_3            4                 23
  CLUS_4           21                163
D71V11, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           18                151
  CLUS_2            4                112
  CLUS_3            8                 66
D71V12, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            4                113
  CLUS_2           19                178
  CLUS_3            7                 38

Clustering(72) Variable = 18q loss
D72V1, multiclass
[1] "Remove cluster labels:" "18Q LOSS CNV"          
clus
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
D72V2, multiclass
[1] "Remove cluster labels:" "18Q LOSS CNV"          
clus
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LJ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
D72V3, multiclass
D72V4, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           30                113
  CLUS_2           10                 74
  CLUS_3            4                146
D72V5, multiclass
D72V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV          8    4
  18Q LOSS WILD-TYPE  113   69
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            8                113
  CLUS_2            4                 69
D72V7, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           23                119
  CLUS_2            1                106
  CLUS_3            4                109
D72V8, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            1                 64
  CLUS_2            0                 92
  CLUS_3            3                 62
  CLUS_4           24                116
D72V9, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           37                170
  CLUS_2            5                139
  CLUS_3            6                126
D72V10, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            4                189
  CLUS_2            6                 73
  CLUS_3            6                 21
  CLUS_4           32                152
D72V11, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           27                142
  CLUS_2            6                110
  CLUS_3           10                 64
D72V12, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            5                112
  CLUS_2           30                167
  CLUS_3            8                 37

Clustering(73) Variable = 19p loss
D73V1, multiclass
[1] "Remove cluster labels:" "19P LOSS CNV"          
clus
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BK-A0CC 
"19P LOSS WILD-TYPE" 
D73V2, multiclass
[1] "Remove cluster labels:" "19P LOSS CNV"          
clus
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 1                 52 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LN         TCGA-AP-A0LT 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A06F         TCGA-AX-A06J         TCGA-AX-A0IW 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AX-A0J1         TCGA-B5-A0JR         TCGA-B5-A0JZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B5-A0K0         TCGA-B5-A0K1         TCGA-B5-A0K4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BG-A0LW         TCGA-BG-A0MI         TCGA-BK-A0C9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BK-A0CC 
"19P LOSS WILD-TYPE" 
D73V3, multiclass
D73V4, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           25                118
  CLUS_2            4                 80
  CLUS_3            1                149
D73V5, multiclass
D73V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS CNV          5    3
  19P LOSS WILD-TYPE  116   70
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            5                116
  CLUS_2            3                 70
D73V7, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           16                126
  CLUS_2            0                107
  CLUS_3            2                111
D73V8, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                 64
  CLUS_2            0                 92
  CLUS_3            0                 65
  CLUS_4           17                123
D73V9, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           27                180
  CLUS_2            2                142
  CLUS_3            4                128
D73V10, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                192
  CLUS_2            4                 75
  CLUS_3            3                 24
  CLUS_4           25                159
D73V11, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           26                143
  CLUS_2            1                115
  CLUS_3            3                 71
D73V12, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            2                115
  CLUS_2           23                174
  CLUS_3            5                 40

Clustering(74) Variable = 19q loss
D74V1, multiclass
[1] "Remove cluster labels:" "19Q LOSS CNV"          
clus
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D74V2, multiclass
[1] "Remove cluster labels:" "19Q LOSS CNV"          
clus
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G2         TCGA-A5-A0G5         TCGA-A5-A0GA 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A5-A0GB         TCGA-A5-A0GE         TCGA-A5-A0GH 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GP         TCGA-A5-A0GU 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A051         TCGA-AP-A052         TCGA-AP-A053 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A054         TCGA-AP-A056         TCGA-AP-A05A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05J         TCGA-AP-A05N 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A05P         TCGA-AP-A0L8         TCGA-AP-A0L9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LG         TCGA-AP-A0LJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D74V3, multiclass
D74V4, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           18                125
  CLUS_2            5                 79
  CLUS_3            1                149
D74V5, multiclass
D74V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS CNV          5    2
  19Q LOSS WILD-TYPE  116   71
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            5                116
  CLUS_2            2                 71
D74V7, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           12                130
  CLUS_2            0                107
  CLUS_3            2                111
D74V8, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            1                 64
  CLUS_2            0                 92
  CLUS_3            1                 64
  CLUS_4           12                128
D74V9, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           21                186
  CLUS_2            2                142
  CLUS_3            4                128
D74V10, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            1                192
  CLUS_2            3                 76
  CLUS_3            3                 24
  CLUS_4           20                164
D74V11, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           21                148
  CLUS_2            1                115
  CLUS_3            2                 72
D74V12, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            2                115
  CLUS_2           17                180
  CLUS_3            5                 40

Clustering(75) Variable = 20p loss
D75V1, multiclass
[1] "Remove cluster labels:" "20P LOSS CNV"          
clus
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G5         TCGA-A5-A0GA         TCGA-A5-A0GB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D75V2, multiclass
[1] "Remove cluster labels:" "20P LOSS CNV"          
clus
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 2                 51 
        TCGA-A5-A0G5         TCGA-A5-A0GA         TCGA-A5-A0GB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A5-A0GE         TCGA-A5-A0GH         TCGA-A5-A0GM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A5-A0GP         TCGA-A5-A0GU         TCGA-AP-A051 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A05A         TCGA-AP-A05D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A05J         TCGA-AP-A05N         TCGA-AP-A05P 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0L8         TCGA-AP-A0L9         TCGA-AP-A0LD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LT         TCGA-AP-A0LV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A05S         TCGA-AX-A05T         TCGA-AX-A05U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A05W         TCGA-AX-A05Y         TCGA-AX-A05Z 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A060         TCGA-AX-A062         TCGA-AX-A063 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A064         TCGA-AX-A06B         TCGA-AX-A06F 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AX-A06J         TCGA-AX-A0IW         TCGA-AX-A0J1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B5-A0JR         TCGA-B5-A0JZ         TCGA-B5-A0K0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B5-A0K1         TCGA-B5-A0K4         TCGA-BG-A0LW 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BG-A0MI         TCGA-BK-A0C9         TCGA-BK-A0CC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D75V3, multiclass
D75V4, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            6                137
  CLUS_2            3                 81
  CLUS_3            1                149
D75V5, multiclass
D75V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS CNV          2    2
  20P LOSS WILD-TYPE  119   71
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            2                119
  CLUS_2            2                 71
D75V7, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            7                135
  CLUS_2            0                107
  CLUS_3            2                111
D75V8, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            2                 63
  CLUS_2            0                 92
  CLUS_3            0                 65
  CLUS_4            7                133
D75V9, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           11                196
  CLUS_2            0                144
  CLUS_3            3                129
D75V10, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            2                191
  CLUS_2            2                 77
  CLUS_3            0                 27
  CLUS_4           10                174
D75V11, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            7                162
  CLUS_2            1                115
  CLUS_3            3                 71
D75V12, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                116
  CLUS_2            9                188
  CLUS_3            1                 44

Clustering(76) Variable = 20q loss
D76V1, multiclass
D76V2, multiclass
D76V3, multiclass
D76V4, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            3                140
  CLUS_2            3                 81
  CLUS_3            0                150
D76V5, multiclass
[1] "Remove cluster labels:" "20Q LOSS CNV"          
clus
      20Q LOSS CNV 20Q LOSS WILD-TYPE 
                 2                192 
        TCGA-A5-A0G1         TCGA-A5-A0G2         TCGA-A5-A0G5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0G9         TCGA-A5-A0GA         TCGA-A5-A0GB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GD         TCGA-A5-A0GE         TCGA-A5-A0GG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GH         TCGA-A5-A0GI         TCGA-A5-A0GJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GM         TCGA-A5-A0GQ         TCGA-A5-A0GR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GU         TCGA-A5-A0GV         TCGA-A5-A0GW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0GX         TCGA-A5-A0R6         TCGA-A5-A0R7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0R8         TCGA-A5-A0R9         TCGA-A5-A0RA 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A5-A0VP         TCGA-A5-A0VQ         TCGA-AP-A051 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A052         TCGA-AP-A053         TCGA-AP-A054 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A056         TCGA-AP-A059         TCGA-AP-A05A 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A05D         TCGA-AP-A05H         TCGA-AP-A05J 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A05N         TCGA-AP-A05O         TCGA-AP-A05P 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LD         TCGA-AP-A0LE         TCGA-AP-A0LF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LG         TCGA-AP-A0LH         TCGA-AP-A0LI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LJ         TCGA-AP-A0LL         TCGA-AP-A0LM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LN         TCGA-AP-A0LP         TCGA-AP-A0LT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AP-A0LV         TCGA-AX-A05S         TCGA-AX-A05T 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A05U         TCGA-AX-A05W         TCGA-AX-A05Y 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A05Z         TCGA-AX-A060         TCGA-AX-A062 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A063         TCGA-AX-A064         TCGA-AX-A06B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A06D         TCGA-AX-A06F         TCGA-AX-A06J 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A06L         TCGA-AX-A0IS         TCGA-AX-A0IW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AX-A0IZ         TCGA-AX-A0J0         TCGA-AX-A0J1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A0JN         TCGA-B5-A0JT         TCGA-B5-A0JY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A0JZ         TCGA-B5-A0K0         TCGA-B5-A0K1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A0K2         TCGA-B5-A0K3         TCGA-B5-A0K4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A0K7         TCGA-B5-A0K9         TCGA-B5-A11E 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A11F         TCGA-B5-A11G         TCGA-B5-A11H 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A11I         TCGA-B5-A11N         TCGA-B5-A11Q 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A11S         TCGA-B5-A11U         TCGA-B5-A11V 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A11W         TCGA-B5-A11Y         TCGA-B5-A11Z 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B5-A121         TCGA-BG-A0LW         TCGA-BG-A0LX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0M0         TCGA-BG-A0M2         TCGA-BG-A0M3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0M4         TCGA-BG-A0M6         TCGA-BG-A0M7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0M8         TCGA-BG-A0M9         TCGA-BG-A0MC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0MG         TCGA-BG-A0MS         TCGA-BG-A0MT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0MU         TCGA-BG-A0RY         TCGA-BG-A0VT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0VV         TCGA-BG-A0W1         TCGA-BG-A0YU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A0YV         TCGA-BG-A186         TCGA-BG-A187 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BG-A18A         TCGA-BG-A18B         TCGA-BG-A18C 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BK-A0C9         TCGA-BK-A0CA         TCGA-BK-A0CB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BK-A0CC         TCGA-BK-A139         TCGA-BK-A13C 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BS-A0T9         TCGA-BS-A0TA         TCGA-BS-A0TC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BS-A0TD         TCGA-BS-A0TG         TCGA-BS-A0TI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BS-A0TJ         TCGA-BS-A0U7         TCGA-BS-A0U8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BS-A0U9         TCGA-BS-A0UF         TCGA-BS-A0UJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-BS-A0V7         TCGA-D1-A0ZP         TCGA-D1-A0ZR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A0ZU         TCGA-D1-A101         TCGA-D1-A102 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A103         TCGA-D1-A15V         TCGA-D1-A15W 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A15X         TCGA-D1-A15Z         TCGA-D1-A160 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A161         TCGA-D1-A163         TCGA-D1-A165 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A167         TCGA-D1-A168         TCGA-D1-A169 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A16B         TCGA-D1-A16D         TCGA-D1-A16E 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A16G         TCGA-D1-A16I         TCGA-D1-A16J 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A16N         TCGA-D1-A16O         TCGA-D1-A16Q 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A16R         TCGA-D1-A16S         TCGA-D1-A16V 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A16X         TCGA-D1-A16Y         TCGA-D1-A175 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A176         TCGA-D1-A177         TCGA-D1-A179 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A17B         TCGA-D1-A17C         TCGA-D1-A17D 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A17F         TCGA-D1-A17H         TCGA-D1-A17K 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A17L         TCGA-D1-A17M         TCGA-D1-A17N 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A17Q         TCGA-D1-A17R         TCGA-D1-A17S 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-D1-A17T         TCGA-D1-A17U         TCGA-DI-A0WH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D76V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS CNV          2    0
  20Q LOSS WILD-TYPE  119   73
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            2                119
  CLUS_2            0                 73
D76V7, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            3                139
  CLUS_2            0                107
  CLUS_3            1                112
D76V8, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            1                 64
  CLUS_2            0                 92
  CLUS_3            0                 65
  CLUS_4            3                137
D76V9, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            5                202
  CLUS_2            0                144
  CLUS_3            2                130
D76V10, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            0                193
  CLUS_2            2                 77
  CLUS_3            0                 27
  CLUS_4            5                179
D76V11, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            5                164
  CLUS_2            0                116
  CLUS_3            1                 73
D76V12, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            0                117
  CLUS_2            5                192
  CLUS_3            1                 44

Clustering(77) Variable = 21q loss
D77V1, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            4                 13
  CLUS_3            0                 12
  CLUS_4            0                 10
D77V2, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            0                 19
  CLUS_2            0                 19
  CLUS_3            4                 11
D77V3, multiclass
D77V4, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           17                126
  CLUS_2            5                 79
  CLUS_3            3                147
D77V5, multiclass
D77V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV          6    5
  21Q LOSS WILD-TYPE  115   68
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            6                115
  CLUS_2            5                 68
D77V7, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           15                127
  CLUS_2            0                107
  CLUS_3            3                110
D77V8, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            1                 64
  CLUS_2            0                 92
  CLUS_3            3                 62
  CLUS_4           14                126
D77V9, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           22                185
  CLUS_2            2                142
  CLUS_3            6                126
D77V10, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            2                191
  CLUS_2            7                 72
  CLUS_3            0                 27
  CLUS_4           21                163
D77V11, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           21                148
  CLUS_2            1                115
  CLUS_3            3                 71
D77V12, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            1                116
  CLUS_2           23                174
  CLUS_3            1                 44

Clustering(78) Variable = 22q loss
D78V1, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            0                 14
  CLUS_2            5                 12
  CLUS_3            0                 12
  CLUS_4            0                 10
D78V2, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            0                 19
  CLUS_2            0                 19
  CLUS_3            5                 10
D78V3, multiclass
D78V4, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           46                 97
  CLUS_2           22                 62
  CLUS_3           10                140
D78V5, multiclass
D78V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS CNV         13    7
  22Q LOSS WILD-TYPE  108   66
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           13                108
  CLUS_2            7                 66
D78V7, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           41                101
  CLUS_2            3                104
  CLUS_3            5                108
D78V8, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            1                 64
  CLUS_2            1                 91
  CLUS_3            3                 62
  CLUS_4           44                 96
D78V9, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           64                143
  CLUS_2           14                130
  CLUS_3            7                125
D78V10, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           13                180
  CLUS_2            8                 71
  CLUS_3            6                 21
  CLUS_4           58                126
D78V11, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           45                124
  CLUS_2           14                102
  CLUS_3           16                 58
D78V12, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           12                105
  CLUS_2           52                145
  CLUS_3           11                 34

Clustering(79) Variable = Xq loss
D79V1, multiclass
D79V2, multiclass
D79V3, multiclass
D79V4, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1          11               132
  CLUS_2           5                79
  CLUS_3           0               150
D79V5, multiclass
D79V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS CNV          2    2
  XQ LOSS WILD-TYPE  119   71
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           2               119
  CLUS_2           2                71
D79V7, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           7               135
  CLUS_2           0               107
  CLUS_3           1               112
D79V8, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                65
  CLUS_2           0                92
  CLUS_3           0                65
  CLUS_4           8               132
D79V9, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1          16               191
  CLUS_2           1               143
  CLUS_3           1               131
D79V10, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0               193
  CLUS_2           1                78
  CLUS_3           1                26
  CLUS_4          16               168
D79V11, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1          12               157
  CLUS_2           0               116
  CLUS_3           3                71
D79V12, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0               117
  CLUS_2          14               183
  CLUS_3           1                44
                           V1                            V2 
                  "MRNA_CNMF"          "MRNA_CHIERARCHICAL" 
                           V3                            V4 
                    "CN_CNMF"            "METHLYATION_CNMF" 
                           V5                            V6 
                  "RPPA_CNMF"          "RPPA_CHIERARCHICAL" 
                           V7                            V8 
               "MRNASEQ_CNMF"       "MRNASEQ_CHIERARCHICAL" 
                           V9                           V10 
                "MIRSEQ_CNMF"        "MIRSEQ_CHIERARCHICAL" 
                          V11                           V12 
         "MIRSEQ_MATURE_CNMF" "MIRSEQ_MATURE_CHIERARCHICAL" 
> q(save="no")
