
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/LUAD-TP/3472668/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/LUAD-TP/3537660/LUAD-TP.transferedmergedcluster.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=LUAD-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=LUAD-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=498, in cluster file=493, common to both=493
[1]  80 493
[1] "1p gain"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
               58               435 
      1P GAIN CNV 1P GAIN WILD-TYPE 
               58               435 
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
              191               302 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
              191               302 
[1] "2p gain"
[1] 3
      2P GAIN CNV 2P GAIN WILD-TYPE 
               50               443 
      2P GAIN CNV 2P GAIN WILD-TYPE 
               50               443 
[1] "2q gain"
[1] 3
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               45               448 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               45               448 
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
               13               480 
      3P GAIN CNV 3P GAIN WILD-TYPE 
               13               480 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               30               463 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               30               463 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
               30               463 
      4P GAIN CNV 4P GAIN WILD-TYPE 
               30               463 
[1] "4q gain"
[1] 3
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
               10               483 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
               10               483 
[1] "5p gain"
[1] 3
      5P GAIN CNV 5P GAIN WILD-TYPE 
              184               309 
      5P GAIN CNV 5P GAIN WILD-TYPE 
              184               309 
[1] "5q gain"
[1] 3
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               60               433 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               60               433 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
               73               420 
      6P GAIN CNV 6P GAIN WILD-TYPE 
               73               420 
[1] "6q gain"
[1] 3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
               19               474 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
               19               474 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
              159               334 
      7P GAIN CNV 7P GAIN WILD-TYPE 
              159               334 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
              112               381 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
              112               381 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
               61               432 
      8P GAIN CNV 8P GAIN WILD-TYPE 
               61               432 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
              149               344 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
              149               344 
[1] "9p gain"
[1] 3
      9P GAIN CNV 9P GAIN WILD-TYPE 
               16               477 
      9P GAIN CNV 9P GAIN WILD-TYPE 
               16               477 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                8               485 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                8               485 
[1] "10p gain"
[1] 3
      10P GAIN CNV 10P GAIN WILD-TYPE 
                51                442 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                51                442 
[1] "10q gain"
[1] 3
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                30                463 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                30                463 
[1] "11p gain"
[1] 3
      11P GAIN CNV 11P GAIN WILD-TYPE 
                36                457 
      11P GAIN CNV 11P GAIN WILD-TYPE 
                36                457 
[1] "11q gain"
[1] 3
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                51                442 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                51                442 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                59                434 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                59                434 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                48                445 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                48                445 
[1] "13q gain"
[1] 3
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                16                477 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                16                477 
[1] "14q gain"
[1] 3
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                59                434 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                59                434 
[1] "15q gain"
[1] 3
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                14                479 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                14                479 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                71                422 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                71                422 
[1] "16q gain"
[1] 3
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                43                450 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                43                450 
[1] "17p gain"
[1] 3
      17P GAIN CNV 17P GAIN WILD-TYPE 
                29                464 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                29                464 
[1] "17q gain"
[1] 3
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                80                413 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                80                413 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                44                449 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                44                449 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                27                466 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                27                466 
[1] "19p gain"
[1] 3
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 6                487 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 6                487 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                24                469 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                24                469 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                63                430 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                63                430 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                78                415 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                78                415 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                43                450 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                43                450 
[1] "22q gain"
[1] 3
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                20                473 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                20                473 
[1] "Xq gain"
[1] 3
      XQ GAIN CNV XQ GAIN WILD-TYPE 
               17               476 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
               17               476 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
               29               464 
      1P LOSS CNV 1P LOSS WILD-TYPE 
               29               464 
[1] "1q loss"
[1] 3
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
               10               483 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
               10               483 
[1] "2p loss"
[1] 3
      2P LOSS CNV 2P LOSS WILD-TYPE 
                6               487 
      2P LOSS CNV 2P LOSS WILD-TYPE 
                6               487 
[1] "2q loss"
[1] 3
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                4               489 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                4               489 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
               96               397 
      3P LOSS CNV 3P LOSS WILD-TYPE 
               96               397 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
               56               437 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
               56               437 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
               40               453 
      4P LOSS CNV 4P LOSS WILD-TYPE 
               40               453 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               47               446 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               47               446 
[1] "5p loss"
[1] 3
      5P LOSS CNV 5P LOSS WILD-TYPE 
               11               482 
      5P LOSS CNV 5P LOSS WILD-TYPE 
               11               482 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               60               433 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               60               433 
[1] "6p loss"
[1] 3
      6P LOSS CNV 6P LOSS WILD-TYPE 
               43               450 
      6P LOSS CNV 6P LOSS WILD-TYPE 
               43               450 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
              112               381 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
              112               381 
[1] "7p loss"
[1] 3
      7P LOSS CNV 7P LOSS WILD-TYPE 
               14               479 
      7P LOSS CNV 7P LOSS WILD-TYPE 
               14               479 
[1] "7q loss"
[1] 3
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
               17               476 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
               17               476 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
              122               371 
      8P LOSS CNV 8P LOSS WILD-TYPE 
              122               371 
[1] "8q loss"
[1] 3
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
               21               472 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
               21               472 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
              142               351 
      9P LOSS CNV 9P LOSS WILD-TYPE 
              142               351 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
              120               373 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
              120               373 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                38                455 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                38                455 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                49                444 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                49                444 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                36                457 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                36                457 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                31                462 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                31                462 
[1] "12p loss"
[1] 3
      12P LOSS CNV 12P LOSS WILD-TYPE 
                40                453 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                40                453 
[1] "12q loss"
[1] 3
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                24                469 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                24                469 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
               115                378 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
               115                378 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                47                446 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                47                446 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                98                395 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                98                395 
[1] "16p loss"
[1] 3
      16P LOSS CNV 16P LOSS WILD-TYPE 
                39                454 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                39                454 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                57                436 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                57                436 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
               118                375 
      17P LOSS CNV 17P LOSS WILD-TYPE 
               118                375 
[1] "17q loss"
[1] 3
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                19                474 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                19                474 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                80                413 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                80                413 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
               112                381 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
               112                381 
[1] "19p loss"
[1] 3
      19P LOSS CNV 19P LOSS WILD-TYPE 
               119                374 
      19P LOSS CNV 19P LOSS WILD-TYPE 
               119                374 
[1] "19q loss"
[1] 3
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                72                421 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                72                421 
[1] "20p loss"
[1] 3
      20P LOSS CNV 20P LOSS WILD-TYPE 
                66                427 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                66                427 
[1] "20q loss"
[1] 3
      20Q LOSS CNV 20Q LOSS WILD-TYPE 
                25                468 
      20Q LOSS CNV 20Q LOSS WILD-TYPE 
                25                468 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                68                425 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                68                425 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                97                396 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                97                396 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
               11               482 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
               11               482 
[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 493 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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 4:'METHLYATION_CNMF':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'MRNASEQ_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'MIRSEQ_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'MIRSEQ_CHIERARCHICAL':	nDistinctValues=3,	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 493 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=3, binary=FALSE, numeric=FALSE
METHLYATION_CNMF, nv=4, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=4, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=9, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CHIERARCHICAL, nv=3, 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           0                 5
  CLUS_2           1                 8
  CLUS_3           2                10
  CLUS_4           1                 5
D1V2, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           2                11
  CLUS_3           1                11
D1V3, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          41               146
  CLUS_2           9               205
  CLUS_3           8                84
D1V4, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           8                78
  CLUS_2          16                92
  CLUS_3          20                90
  CLUS_4           5                95
D1V5, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          14                71
  CLUS_2           4                71
  CLUS_3           8                67
D1V6, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           1                22
  CLUS_2          17                72
  CLUS_3           3                62
  CLUS_4           5                53
D1V7, multiclass
D1V8, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          18               140
  CLUS_2          18                87
  CLUS_3          14               114
D1V9, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          18               153
  CLUS_2          25               173
  CLUS_3          14                84
D1V10, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          19               145
  CLUS_2          29               215
  CLUS_3           9                50
D1V11, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          19               138
  CLUS_2          22               152
  CLUS_3           9                64
D1V12, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          22               131
  CLUS_2           3                43
  CLUS_3          25               180

Clustering(2) Variable = 1q gain
D2V1, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           3                 6
  CLUS_3           5                 7
  CLUS_4           2                 4
D2V2, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           2                 5
  CLUS_2           5                 8
  CLUS_3           3                 9
D2V3, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          82               105
  CLUS_2          69               145
  CLUS_3          40                52
D2V4, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          37                49
  CLUS_2          49                59
  CLUS_3          51                59
  CLUS_4          16                84
D2V5, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          30                55
  CLUS_2          33                42
  CLUS_3          21                54
D2V6, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1           5                18
  CLUS_2          34                55
  CLUS_3          19                46
  CLUS_4          26                32
D2V7, multiclass
D2V8, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          66                92
  CLUS_2          39                66
  CLUS_3          47                81
D2V9, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          64               107
  CLUS_2          79               119
  CLUS_3          32                66
D2V10, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          65                99
  CLUS_2          91               153
  CLUS_3          19                40
D2V11, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          63                94
  CLUS_2          68               106
  CLUS_3          23                50
D2V12, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          65                88
  CLUS_2          11                35
  CLUS_3          78               127

Clustering(3) Variable = 2p gain
D3V1, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           2                 3
  CLUS_2           0                 9
  CLUS_3           1                11
  CLUS_4           3                 3
D3V2, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           4                 3
  CLUS_2           1                12
  CLUS_3           1                11
D3V3, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          28               159
  CLUS_2           4               210
  CLUS_3          18                74
D3V4, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           4                82
  CLUS_2          25                83
  CLUS_3           8               102
  CLUS_4           2                98
D3V5, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           7                78
  CLUS_2           8                67
  CLUS_3          15                60
D3V6, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           1                22
  CLUS_2           7                82
  CLUS_3          15                50
  CLUS_4           7                51
D3V7, multiclass
D3V8, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          11               147
  CLUS_2           7                98
  CLUS_3          26               102
D3V9, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          10               161
  CLUS_2          34               164
  CLUS_3           5                93
D3V10, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          10               154
  CLUS_2          36               208
  CLUS_3           3                56
D3V11, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           8               149
  CLUS_2          27               147
  CLUS_3           4                69
D3V12, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           8               145
  CLUS_2           4                42
  CLUS_3          27               178

Clustering(4) Variable = 2q gain
D4V1, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           0                 9
  CLUS_3           1                11
  CLUS_4           3                 3
D4V2, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           1                12
  CLUS_3           0                12
D4V3, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          20               167
  CLUS_2           6               208
  CLUS_3          19                73
D4V4, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           4                82
  CLUS_2          25                83
  CLUS_3           9               101
  CLUS_4           0               100
D4V5, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           5                80
  CLUS_2           9                66
  CLUS_3          10                65
D4V6, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           1                22
  CLUS_2           6                83
  CLUS_3          10                55
  CLUS_4           7                51
D4V7, multiclass
D4V8, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          13               145
  CLUS_2           6                99
  CLUS_3          21               107
D4V9, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          10               161
  CLUS_2          32               166
  CLUS_3           3                95
D4V10, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          10               154
  CLUS_2          34               210
  CLUS_3           1                58
D4V11, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           8               149
  CLUS_2          29               145
  CLUS_3           2                71
D4V12, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           8               145
  CLUS_2           2                44
  CLUS_3          29               176

Clustering(5) Variable = 3p gain
D5V1, multiclass
D5V2, multiclass
D5V3, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           8               179
  CLUS_2           1               213
  CLUS_3           4                88
D5V4, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           1                85
  CLUS_2           4               104
  CLUS_3           7               103
  CLUS_4           1                99
D5V5, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           4                81
  CLUS_2           0                75
  CLUS_3           4                71
D5V6, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           2                87
  CLUS_3           5                60
  CLUS_4           1                57
D5V7, multiclass
D5V8, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0               158
  CLUS_2           7                98
  CLUS_3           5               123
D5V9, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           4               167
  CLUS_2           6               192
  CLUS_3           3                95
D5V10, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           3               161
  CLUS_2           8               236
  CLUS_3           2                57
D5V11, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           4               153
  CLUS_2           6               168
  CLUS_3           3                70
D5V12, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           3               150
  CLUS_2           1                45
  CLUS_3           9               196

Clustering(6) Variable = 3q gain
D6V1, multiclass
[1] "Remove cluster labels:" "3Q GAIN CNV"           
clus
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D6V2, multiclass
[1] "Remove cluster labels:" "3Q GAIN CNV"           
clus
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D6V3, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          14               173
  CLUS_2           5               209
  CLUS_3          11                81
D6V4, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           1                85
  CLUS_2          13                95
  CLUS_3           9               101
  CLUS_4           4                96
D6V5, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           5                80
  CLUS_2           2                73
  CLUS_3           9                66
D6V6, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           3                86
  CLUS_3          10                55
  CLUS_4           3                55
D6V7, multiclass
D6V8, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           5               153
  CLUS_2           8                97
  CLUS_3          11               117
D6V9, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           7               164
  CLUS_2          19               179
  CLUS_3           3                95
D6V10, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           7               157
  CLUS_2          19               225
  CLUS_3           3                56
D6V11, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           6               151
  CLUS_2          17               157
  CLUS_3           4                69
D6V12, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           7               146
  CLUS_2           1                45
  CLUS_3          19               186

Clustering(7) Variable = 4p gain
D7V1, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           0                 9
  CLUS_3           2                10
  CLUS_4           1                 5
D7V2, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           2                11
  CLUS_3           0                12
D7V3, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1          22               165
  CLUS_2           4               210
  CLUS_3           4                88
D7V4, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           6                80
  CLUS_2          12                96
  CLUS_3           5               105
  CLUS_4           2                98
D7V5, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           6                79
  CLUS_2           2                73
  CLUS_3           9                66
D7V6, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           7                82
  CLUS_3           9                56
  CLUS_4           1                57
D7V7, multiclass
D7V8, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           7               151
  CLUS_2           9                96
  CLUS_3           9               119
D7V9, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           8               163
  CLUS_2          14               184
  CLUS_3           7                91
D7V10, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           7               157
  CLUS_2          18               226
  CLUS_3           4                55
D7V11, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           9               148
  CLUS_2          13               161
  CLUS_3           3                70
D7V12, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           7               146
  CLUS_2           2                44
  CLUS_3          16               189

Clustering(8) Variable = 4q gain
D8V1, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-55-1596        TCGA-64-1676 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-64-1677        TCGA-64-1678        TCGA-67-3770        TCGA-67-3771 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V2, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-55-1596        TCGA-64-1676 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-64-1677        TCGA-64-1678        TCGA-67-3770        TCGA-67-3771 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V3, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           8               179
  CLUS_2           1               213
  CLUS_3           1                91
D8V4, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           2                84
  CLUS_2           2               106
  CLUS_3           2               108
  CLUS_4           1                99
D8V5, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           1                84
  CLUS_2           1                74
  CLUS_3           4                71
D8V6, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           1                88
  CLUS_3           4                61
  CLUS_4           1                57
D8V7, multiclass
D8V8, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           2               156
  CLUS_2           4               101
  CLUS_3           2               126
D8V9, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           1               170
  CLUS_2           4               194
  CLUS_3           4                94
D8V10, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           1               163
  CLUS_2           6               238
  CLUS_3           2                57
D8V11, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           1               156
  CLUS_2           5               169
  CLUS_3           1                72
D8V12, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           0               153
  CLUS_2           2                44
  CLUS_3           5               200

Clustering(9) Variable = 5p gain
D9V1, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           3                 2
  CLUS_2           2                 7
  CLUS_3           6                 6
  CLUS_4           2                 4
D9V2, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           7                 6
  CLUS_3           3                 9
D9V3, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1         105                82
  CLUS_2          46               168
  CLUS_3          33                59
D9V4, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          30                56
  CLUS_2          49                59
  CLUS_3          47                63
  CLUS_4          28                72
D9V5, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          38                47
  CLUS_2          30                45
  CLUS_3          23                52
D9V6, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1           6                17
  CLUS_2          36                53
  CLUS_3          27                38
  CLUS_4          22                36
D9V7, multiclass
D9V8, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          50               108
  CLUS_2          51                54
  CLUS_3          47                81
D9V9, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          57               114
  CLUS_2          86               112
  CLUS_3          35                63
D9V10, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          52               112
  CLUS_2          99               145
  CLUS_3          27                32
D9V11, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          55               102
  CLUS_2          74               100
  CLUS_3          25                48
D9V12, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          50               103
  CLUS_2          20                26
  CLUS_3          84               121

Clustering(10) Variable = 5q gain
D10V1, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           3                 2
  CLUS_2           0                 9
  CLUS_3           4                 8
  CLUS_4           0                 6
D10V2, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           4                 9
  CLUS_3           2                10
D10V3, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          31               156
  CLUS_2          20               194
  CLUS_3           9                83
D10V4, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          20                66
  CLUS_2          12                96
  CLUS_3           9               101
  CLUS_4           5                95
D10V5, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          12                73
  CLUS_2          10                65
  CLUS_3           6                69
D10V6, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2          13                76
  CLUS_3           6                59
  CLUS_4           9                49
D10V7, multiclass
D10V8, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          25               133
  CLUS_2          12                93
  CLUS_3           8               120
D10V9, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          23               148
  CLUS_2          20               178
  CLUS_3          14                84
D10V10, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          25               139
  CLUS_2          23               221
  CLUS_3           9                50
D10V11, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          21               136
  CLUS_2          15               159
  CLUS_3          10                63
D10V12, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          19               134
  CLUS_2           8                38
  CLUS_3          19               186

Clustering(11) Variable = 6p gain
D11V1, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           1                 4
  CLUS_2           0                 9
  CLUS_3           3                 9
  CLUS_4           2                 4
D11V2, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           3                10
  CLUS_3           0                12
D11V3, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          36               151
  CLUS_2          20               194
  CLUS_3          17                75
D11V4, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          13                73
  CLUS_2          33                75
  CLUS_3          10               100
  CLUS_4           3                97
D11V5, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           6                79
  CLUS_2          18                57
  CLUS_3          10                65
D11V6, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           2                21
  CLUS_2           9                80
  CLUS_3          11                54
  CLUS_4          12                46
D11V7, multiclass
D11V8, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          30               128
  CLUS_2          12                93
  CLUS_3          19               109
D11V9, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          22               149
  CLUS_2          37               161
  CLUS_3           9                89
D11V10, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          21               143
  CLUS_2          41               203
  CLUS_3           6                53
D11V11, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          20               137
  CLUS_2          32               142
  CLUS_3           7                66
D11V12, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          19               134
  CLUS_2           3                43
  CLUS_3          37               168

Clustering(12) Variable = 6q gain
D12V1, multiclass
D12V2, multiclass
D12V3, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           9               178
  CLUS_2           4               210
  CLUS_3           6                86
D12V4, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           3                83
  CLUS_2          11                97
  CLUS_3           4               106
  CLUS_4           0               100
D12V5, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1                84
  CLUS_2           3                72
  CLUS_3           6                69
D12V6, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           1                22
  CLUS_2           3                86
  CLUS_3           6                59
  CLUS_4           0                58
D12V7, multiclass
D12V8, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           5               153
  CLUS_2           5               100
  CLUS_3           7               121
D12V9, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           3               168
  CLUS_2          12               186
  CLUS_3           4                94
D12V10, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           2               162
  CLUS_2          15               229
  CLUS_3           2                57
D12V11, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           4               153
  CLUS_2          10               164
  CLUS_3           4                69
D12V12, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           3               150
  CLUS_2           1                45
  CLUS_3          14               191

Clustering(13) Variable = 7p gain
D13V1, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           1                 4
  CLUS_2           2                 7
  CLUS_3           3                 9
  CLUS_4           0                 6
D13V2, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           3                10
  CLUS_3           3                 9
D13V3, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1         108                79
  CLUS_2          29               185
  CLUS_3          22                70
D13V4, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          25                61
  CLUS_2          48                60
  CLUS_3          46                64
  CLUS_4          20                80
D13V5, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          38                47
  CLUS_2          13                62
  CLUS_3          35                40
D13V6, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1           5                18
  CLUS_2          41                48
  CLUS_3          27                38
  CLUS_4          13                45
D13V7, multiclass
D13V8, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          40               118
  CLUS_2          59                46
  CLUS_3          36                92
D13V9, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          39               132
  CLUS_2          71               127
  CLUS_3          45                53
D13V10, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          40               124
  CLUS_2          87               157
  CLUS_3          28                31
D13V11, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          38               119
  CLUS_2          68               106
  CLUS_3          33                40
D13V12, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          40               113
  CLUS_2          26                20
  CLUS_3          73               132

Clustering(14) Variable = 7q gain
D14V1, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           3                 6
  CLUS_3           1                11
  CLUS_4           1                 5
D14V2, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           1                12
  CLUS_3           3                 9
D14V3, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          72               115
  CLUS_2          24               190
  CLUS_3          16                76
D14V4, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          17                69
  CLUS_2          26                82
  CLUS_3          37                73
  CLUS_4          16                84
D14V5, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          28                57
  CLUS_2          13                62
  CLUS_3          19                56
D14V6, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1           4                19
  CLUS_2          29                60
  CLUS_3          14                51
  CLUS_4          13                45
D14V7, multiclass
D14V8, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          29               129
  CLUS_2          45                60
  CLUS_3          24               104
D14V9, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          32               139
  CLUS_2          49               149
  CLUS_3          28                70
D14V10, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          31               133
  CLUS_2          62               182
  CLUS_3          16                43
D14V11, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          27               130
  CLUS_2          46               128
  CLUS_3          23                50
D14V12, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          29               124
  CLUS_2          15                31
  CLUS_3          52               153

Clustering(15) Variable = 8p gain
D15V1, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           1                 8
  CLUS_3           1                11
  CLUS_4           1                 5
D15V2, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           2                11
  CLUS_3           0                12
D15V3, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          14               173
  CLUS_2          14               200
  CLUS_3          33                59
D15V4, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           8                78
  CLUS_2          23                85
  CLUS_3          14                96
  CLUS_4           5                95
D15V5, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          13                72
  CLUS_2           7                68
  CLUS_3          12                63
D15V6, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           1                22
  CLUS_2          12                77
  CLUS_3          11                54
  CLUS_4           8                50
D15V7, multiclass
D15V8, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          17               141
  CLUS_2           5               100
  CLUS_3          23               105
D15V9, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          15               156
  CLUS_2          27               171
  CLUS_3          15                83
D15V10, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          13               151
  CLUS_2          36               208
  CLUS_3           8                51
D15V11, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          19               138
  CLUS_2          24               150
  CLUS_3           8                65
D15V12, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          12               141
  CLUS_2           6                40
  CLUS_3          33               172

Clustering(16) Variable = 8q gain
D16V1, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           1                 4
  CLUS_2           3                 6
  CLUS_3           1                11
  CLUS_4           4                 2
D16V2, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           4                 3
  CLUS_2           2                11
  CLUS_3           3                 9
D16V3, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          65               122
  CLUS_2          22               192
  CLUS_3          62                30
D16V4, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          15                71
  CLUS_2          52                56
  CLUS_3          40                70
  CLUS_4          16                84
D16V5, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          29                56
  CLUS_2          16                59
  CLUS_3          31                44
D16V6, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1           4                19
  CLUS_2          35                54
  CLUS_3          27                38
  CLUS_4          10                48
D16V7, multiclass
D16V8, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          32               126
  CLUS_2          33                72
  CLUS_3          52                76
D16V9, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          26               145
  CLUS_2          82               116
  CLUS_3          34                64
D16V10, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          27               137
  CLUS_2         101               143
  CLUS_3          14                45
D16V11, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          34               123
  CLUS_2          69               105
  CLUS_3          21                52
D16V12, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          28               125
  CLUS_2          12                34
  CLUS_3          84               121

Clustering(17) Variable = 9p gain
D17V1, multiclass
D17V2, multiclass
D17V3, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           9               178
  CLUS_2           3               211
  CLUS_3           4                88
D17V4, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1                85
  CLUS_2           8               100
  CLUS_3           6               104
  CLUS_4           0               100
D17V5, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2                83
  CLUS_2           2                73
  CLUS_3           1                74
D17V6, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           2                87
  CLUS_3           1                64
  CLUS_4           2                56
D17V7, multiclass
D17V8, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3               155
  CLUS_2           6                99
  CLUS_3           4               124
D17V9, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3               168
  CLUS_2           9               189
  CLUS_3           3                95
D17V10, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2               162
  CLUS_2          11               233
  CLUS_3           2                57
D17V11, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2               155
  CLUS_2          11               163
  CLUS_3           2                71
D17V12, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3               150
  CLUS_2           1                45
  CLUS_3          11               194

Clustering(18) Variable = 9q gain
D18V1, multiclass
D18V2, multiclass
D18V3, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           7               180
  CLUS_2           1               213
  CLUS_3           0                92
D18V4, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                84
  CLUS_2           4               104
  CLUS_3           2               108
  CLUS_4           0               100
D18V5, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                85
  CLUS_2           2                73
  CLUS_3           2                73
D18V6, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           0                89
  CLUS_3           2                63
  CLUS_4           2                56
D18V7, multiclass
D18V8, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           3               155
  CLUS_2           2               103
  CLUS_3           3               125
D18V9, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1               170
  CLUS_2           4               194
  CLUS_3           3                95
D18V10, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1               163
  CLUS_2           5               239
  CLUS_3           2                57
D18V11, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0               157
  CLUS_2           5               169
  CLUS_3           3                70
D18V12, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1               152
  CLUS_2           2                44
  CLUS_3           5               200

Clustering(19) Variable = 10p gain
D19V1, multiclass
[1] "Remove cluster labels:" "10P GAIN CNV"          
clus
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1680         TCGA-67-3770 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-67-3774 
"10P GAIN WILD-TYPE" 
D19V2, multiclass
[1] "Remove cluster labels:" "10P GAIN CNV"          
clus
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1680         TCGA-67-3770 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-67-3774 
"10P GAIN WILD-TYPE" 
D19V3, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           26                161
  CLUS_2           11                203
  CLUS_3           14                 78
D19V4, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            4                 82
  CLUS_2           19                 89
  CLUS_3           17                 93
  CLUS_4            3                 97
D19V5, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            6                 79
  CLUS_2           11                 64
  CLUS_3           12                 63
D19V6, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            4                 19
  CLUS_2            6                 83
  CLUS_3           11                 54
  CLUS_4            8                 50
D19V7, multiclass
D19V8, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           12                146
  CLUS_2           10                 95
  CLUS_3           20                108
D19V9, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           15                156
  CLUS_2           27                171
  CLUS_3            5                 93
D19V10, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           14                150
  CLUS_2           30                214
  CLUS_3            3                 56
D19V11, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           18                139
  CLUS_2           25                149
  CLUS_3            1                 72
D19V12, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           16                137
  CLUS_2            1                 45
  CLUS_3           27                178

Clustering(20) Variable = 10q gain
D20V1, multiclass
D20V2, multiclass
D20V3, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           13                174
  CLUS_2            9                205
  CLUS_3            8                 84
D20V4, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            4                 82
  CLUS_2           13                 95
  CLUS_3            5                105
  CLUS_4            0                100
D20V5, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            4                 81
  CLUS_2            7                 68
  CLUS_3            4                 71
D20V6, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            2                 21
  CLUS_2            3                 86
  CLUS_3            3                 62
  CLUS_4            7                 51
D20V7, multiclass
D20V8, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           11                147
  CLUS_2            3                102
  CLUS_3            9                119
D20V9, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           11                160
  CLUS_2           11                187
  CLUS_3            4                 94
D20V10, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           11                153
  CLUS_2           14                230
  CLUS_3            1                 58
D20V11, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            9                148
  CLUS_2           12                162
  CLUS_3            2                 71
D20V12, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           10                143
  CLUS_2            0                 46
  CLUS_3           13                192

Clustering(21) Variable = 11p gain
D21V1, multiclass
[1] "Remove cluster labels:" "11P GAIN CNV"          
clus
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1595 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-67-3774 
"11P GAIN WILD-TYPE" 
D21V2, multiclass
[1] "Remove cluster labels:" "11P GAIN CNV"          
clus
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1595 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-67-3774 
"11P GAIN WILD-TYPE" 
D21V3, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1           17                170
  CLUS_2            8                206
  CLUS_3           11                 81
D21V4, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            5                 81
  CLUS_2           12                 96
  CLUS_3           10                100
  CLUS_4            2                 98
D21V5, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            5                 80
  CLUS_2            3                 72
  CLUS_3            9                 66
D21V6, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            7                 82
  CLUS_3            6                 59
  CLUS_4            4                 54
D21V7, multiclass
D21V8, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            9                149
  CLUS_2            9                 96
  CLUS_3           13                115
D21V9, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            6                165
  CLUS_2           19                179
  CLUS_3           10                 88
D21V10, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            7                157
  CLUS_2           22                222
  CLUS_3            6                 53
D21V11, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            5                152
  CLUS_2           17                157
  CLUS_3            7                 66
D21V12, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            7                146
  CLUS_2            4                 42
  CLUS_3           18                187

Clustering(22) Variable = 11q gain
D22V1, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            1                  8
  CLUS_3            0                 12
  CLUS_4            2                  4
D22V2, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            1                 12
  CLUS_3            0                 12
D22V3, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1           29                158
  CLUS_2            9                205
  CLUS_3           13                 79
D22V4, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            5                 81
  CLUS_2           17                 91
  CLUS_3           15                 95
  CLUS_4            5                 95
D22V5, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            8                 77
  CLUS_2            3                 72
  CLUS_3           17                 58
D22V6, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2           11                 78
  CLUS_3           13                 52
  CLUS_4            4                 54
D22V7, multiclass
D22V8, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            8                150
  CLUS_2           17                 88
  CLUS_3           20                108
D22V9, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            8                163
  CLUS_2           28                170
  CLUS_3           13                 85
D22V10, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            9                155
  CLUS_2           33                211
  CLUS_3            7                 52
D22V11, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            7                150
  CLUS_2           25                149
  CLUS_3           10                 63
D22V12, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            9                144
  CLUS_2            5                 41
  CLUS_3           28                177

Clustering(23) Variable = 12p gain
D23V1, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            1                  8
  CLUS_3            1                 11
  CLUS_4            2                  4
D23V2, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            3                  4
  CLUS_2            1                 12
  CLUS_3            1                 11
D23V3, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           30                157
  CLUS_2            7                207
  CLUS_3           22                 70
D23V4, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            2                 84
  CLUS_2           25                 83
  CLUS_3           10                100
  CLUS_4            8                 92
D23V5, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           12                 73
  CLUS_2            5                 70
  CLUS_3           12                 63
D23V6, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2           11                 78
  CLUS_3           12                 53
  CLUS_4            6                 52
D23V7, multiclass
D23V8, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            9                149
  CLUS_2           12                 93
  CLUS_3           27                101
D23V9, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            9                162
  CLUS_2           37                161
  CLUS_3           10                 88
D23V10, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           12                152
  CLUS_2           41                203
  CLUS_3            3                 56
D23V11, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            6                151
  CLUS_2           31                143
  CLUS_3            8                 65
D23V12, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           10                143
  CLUS_2            3                 43
  CLUS_3           32                173

Clustering(24) Variable = 12q gain
D24V1, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            1                  8
  CLUS_3            1                 11
  CLUS_4            2                  4
D24V2, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            3                  4
  CLUS_2            1                 12
  CLUS_3            1                 11
D24V3, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           20                167
  CLUS_2            8                206
  CLUS_3           20                 72
D24V4, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            1                 85
  CLUS_2           20                 88
  CLUS_3            7                103
  CLUS_4            6                 94
D24V5, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            8                 77
  CLUS_2            4                 71
  CLUS_3           11                 64
D24V6, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            8                 81
  CLUS_3           11                 54
  CLUS_4            4                 54
D24V7, multiclass
D24V8, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            8                150
  CLUS_2            8                 97
  CLUS_3           23                105
D24V9, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            9                162
  CLUS_2           29                169
  CLUS_3            7                 91
D24V10, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           10                154
  CLUS_2           31                213
  CLUS_3            4                 55
D24V11, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            5                152
  CLUS_2           22                152
  CLUS_3            7                 66
D24V12, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            8                145
  CLUS_2            4                 42
  CLUS_3           22                183

Clustering(25) Variable = 13q gain
D25V1, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            0                  9
  CLUS_3            1                 11
  CLUS_4            2                  4
D25V2, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            1                 12
  CLUS_3            0                 12
D25V3, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            7                180
  CLUS_2            5                209
  CLUS_3            4                 88
D25V4, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            3                 83
  CLUS_2            8                100
  CLUS_3            1                109
  CLUS_4            0                100
D25V5, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            2                 83
  CLUS_2            3                 72
  CLUS_3            6                 69
D25V6, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            2                 87
  CLUS_3            6                 59
  CLUS_4            3                 55
D25V7, multiclass
D25V8, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            6                152
  CLUS_2            1                104
  CLUS_3            8                120
D25V9, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            5                166
  CLUS_2            8                190
  CLUS_3            2                 96
D25V10, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            4                160
  CLUS_2           11                233
  CLUS_3            0                 59
D25V11, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            5                152
  CLUS_2            5                169
  CLUS_3            2                 71
D25V12, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            4                149
  CLUS_2            0                 46
  CLUS_3            8                197

Clustering(26) Variable = 14q gain
D26V1, multiclass
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2661         TCGA-44-2662         TCGA-44-2665 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"14Q GAIN WILD-TYPE" 
D26V2, multiclass
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2661         TCGA-44-2662         TCGA-44-2665 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"14Q GAIN WILD-TYPE" 
D26V3, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           27                160
  CLUS_2            9                205
  CLUS_3           23                 69
D26V4, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            8                 78
  CLUS_2           30                 78
  CLUS_3           10                100
  CLUS_4            4                 96
D26V5, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            8                 77
  CLUS_2            8                 67
  CLUS_3           15                 60
D26V6, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            2                 21
  CLUS_2           13                 76
  CLUS_3           11                 54
  CLUS_4            5                 53
D26V7, multiclass
D26V8, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           14                144
  CLUS_2           10                 95
  CLUS_3           25                103
D26V9, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           10                161
  CLUS_2           30                168
  CLUS_3           15                 83
D26V10, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            7                157
  CLUS_2           38                206
  CLUS_3           10                 49
D26V11, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           10                147
  CLUS_2           33                141
  CLUS_3            9                 64
D26V12, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           11                142
  CLUS_2            7                 39
  CLUS_3           34                171

Clustering(27) Variable = 15q gain
D27V1, multiclass
[1] "Remove cluster labels:" "15Q GAIN CNV"          
clus
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1595 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"15Q GAIN WILD-TYPE" 
D27V2, multiclass
[1] "Remove cluster labels:" "15Q GAIN CNV"          
clus
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1595 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"15Q GAIN WILD-TYPE" 
D27V3, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            7                180
  CLUS_2            5                209
  CLUS_3            2                 90
D27V4, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            2                 84
  CLUS_2            4                104
  CLUS_3            4                106
  CLUS_4            0                100
D27V5, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            2                 83
  CLUS_2            3                 72
  CLUS_3            3                 72
D27V6, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            4                 85
  CLUS_3            1                 64
  CLUS_4            3                 55
D27V7, multiclass
D27V8, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            7                151
  CLUS_2            1                104
  CLUS_3            6                122
D27V9, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            6                165
  CLUS_2            6                192
  CLUS_3            1                 97
D27V10, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            7                157
  CLUS_2            5                239
  CLUS_3            1                 58
D27V11, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            5                152
  CLUS_2            3                171
  CLUS_3            2                 71
D27V12, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            7                146
  CLUS_2            0                 46
  CLUS_3            3                202

Clustering(28) Variable = 16p gain
D28V1, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            2                  3
  CLUS_2            1                  8
  CLUS_3            2                 10
  CLUS_4            0                  6
D28V2, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            2                 11
  CLUS_3            3                  9
D28V3, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           40                147
  CLUS_2           22                192
  CLUS_3            9                 83
D28V4, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           21                 65
  CLUS_2           19                 89
  CLUS_3           10                100
  CLUS_4            5                 95
D28V5, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           17                 68
  CLUS_2            6                 69
  CLUS_3            8                 67
D28V6, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            3                 20
  CLUS_2           15                 74
  CLUS_3            8                 57
  CLUS_4            5                 53
D28V7, multiclass
D28V8, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           31                127
  CLUS_2           15                 90
  CLUS_3           10                118
D28V9, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           25                146
  CLUS_2           22                176
  CLUS_3           18                 80
D28V10, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           27                137
  CLUS_2           27                217
  CLUS_3           11                 48
D28V11, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           25                132
  CLUS_2           18                156
  CLUS_3           13                 60
D28V12, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           25                128
  CLUS_2            6                 40
  CLUS_3           25                180

Clustering(29) Variable = 16q gain
D29V1, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            2                  7
  CLUS_3            0                 12
  CLUS_4            0                  6
D29V2, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            0                 13
  CLUS_3            3                  9
D29V3, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           25                162
  CLUS_2           14                200
  CLUS_3            4                 88
D29V4, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           14                 72
  CLUS_2            9                 99
  CLUS_3            7                103
  CLUS_4            4                 96
D29V5, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           12                 73
  CLUS_2            2                 73
  CLUS_3            8                 67
D29V6, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            1                 22
  CLUS_2           13                 76
  CLUS_3            7                 58
  CLUS_4            1                 57
D29V7, multiclass
D29V8, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           19                139
  CLUS_2           11                 94
  CLUS_3            8                120
D29V9, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           15                156
  CLUS_2           13                185
  CLUS_3           12                 86
D29V10, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           14                150
  CLUS_2           17                227
  CLUS_3            9                 50
D29V11, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           16                141
  CLUS_2           11                163
  CLUS_3            8                 65
D29V12, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           15                138
  CLUS_2            4                 42
  CLUS_3           16                189

Clustering(30) Variable = 17p gain
D30V1, multiclass
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-67-3770         TCGA-67-3771 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D30V2, multiclass
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-67-3770         TCGA-67-3771 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D30V3, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            9                178
  CLUS_2            4                210
  CLUS_3           16                 76
D30V4, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            3                 83
  CLUS_2           16                 92
  CLUS_3            3                107
  CLUS_4            1                 99
D30V5, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            5                 80
  CLUS_2            2                 73
  CLUS_3            3                 72
D30V6, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            2                 87
  CLUS_3            3                 62
  CLUS_4            4                 54
D30V7, multiclass
D30V8, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            8                150
  CLUS_2            7                 98
  CLUS_3           12                116
D30V9, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            8                163
  CLUS_2           18                180
  CLUS_3            2                 96
D30V10, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            8                156
  CLUS_2           19                225
  CLUS_3            1                 58
D30V11, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            7                150
  CLUS_2           14                160
  CLUS_3            2                 71
D30V12, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            8                145
  CLUS_2            1                 45
  CLUS_3           14                191

Clustering(31) Variable = 17q gain
D31V1, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            3                  2
  CLUS_2            1                  8
  CLUS_3            1                 11
  CLUS_4            0                  6
D31V2, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            1                 12
  CLUS_3            3                  9
D31V3, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           44                143
  CLUS_2           10                204
  CLUS_3           26                 66
D31V4, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            7                 79
  CLUS_2           33                 75
  CLUS_3           23                 87
  CLUS_4            4                 96
D31V5, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           15                 70
  CLUS_2            8                 67
  CLUS_3           13                 62
D31V6, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            1                 22
  CLUS_2           16                 73
  CLUS_3           13                 52
  CLUS_4            6                 52
D31V7, multiclass
D31V8, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           22                136
  CLUS_2           26                 79
  CLUS_3           19                109
D31V9, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           19                152
  CLUS_2           43                155
  CLUS_3           15                 83
D31V10, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           19                145
  CLUS_2           51                193
  CLUS_3            7                 52
D31V11, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           19                138
  CLUS_2           37                137
  CLUS_3           11                 62
D31V12, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           18                135
  CLUS_2            8                 38
  CLUS_3           41                164

Clustering(32) Variable = 18p gain
D32V1, multiclass
[1] "Remove cluster labels:" "18P GAIN CNV"          
clus
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-67-3774 
"18P GAIN WILD-TYPE" 
D32V2, multiclass
[1] "Remove cluster labels:" "18P GAIN CNV"          
clus
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-67-3774 
"18P GAIN WILD-TYPE" 
D32V3, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1           23                164
  CLUS_2            4                210
  CLUS_3           17                 75
D32V4, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            3                 83
  CLUS_2           22                 86
  CLUS_3           11                 99
  CLUS_4            4                 96
D32V5, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            4                 81
  CLUS_2           10                 65
  CLUS_3            6                 69
D32V6, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            5                 84
  CLUS_3            6                 59
  CLUS_4            8                 50
D32V7, multiclass
D32V8, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            9                149
  CLUS_2           11                 94
  CLUS_3           18                110
D32V9, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            8                163
  CLUS_2           27                171
  CLUS_3            9                 89
D32V10, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            9                155
  CLUS_2           32                212
  CLUS_3            3                 56
D32V11, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            9                148
  CLUS_2           26                148
  CLUS_3            5                 68
D32V12, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            7                146
  CLUS_2            3                 43
  CLUS_3           30                175

Clustering(33) Variable = 18q gain
D33V1, multiclass
[1] "Remove cluster labels:" "18Q GAIN CNV"          
clus
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-64-1680         TCGA-67-3770         TCGA-67-3771 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D33V2, multiclass
[1] "Remove cluster labels:" "18Q GAIN CNV"          
clus
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-64-1680         TCGA-67-3770         TCGA-67-3771 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D33V3, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1           14                173
  CLUS_2            1                213
  CLUS_3           12                 80
D33V4, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                 84
  CLUS_2           15                 93
  CLUS_3            4                106
  CLUS_4            2                 98
D33V5, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                 83
  CLUS_2            4                 71
  CLUS_3            8                 67
D33V6, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            1                 88
  CLUS_3            7                 58
  CLUS_4            5                 53
D33V7, multiclass
D33V8, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            3                155
  CLUS_2            6                 99
  CLUS_3           14                114
D33V9, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            5                166
  CLUS_2           16                182
  CLUS_3            6                 92
D33V10, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            5                159
  CLUS_2           20                224
  CLUS_3            2                 57
D33V11, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            4                153
  CLUS_2           15                159
  CLUS_3            4                 69
D33V12, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            3                150
  CLUS_2            1                 45
  CLUS_3           19                186

Clustering(34) Variable = 19p gain
D34V1, multiclass
[1] "Remove cluster labels:" "19P GAIN CNV"          
clus
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2666 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2668         TCGA-44-3398         TCGA-44-3918 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-3919         TCGA-44-4112         TCGA-55-1592 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-55-1594         TCGA-55-1595         TCGA-55-1596 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-64-1676         TCGA-64-1677         TCGA-64-1678 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-64-1680         TCGA-67-3770         TCGA-67-3771 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D34V2, multiclass
[1] "Remove cluster labels:" "19P GAIN CNV"          
clus
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2666 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-2668         TCGA-44-3398         TCGA-44-3918 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-44-3919         TCGA-44-4112         TCGA-55-1592 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-55-1594         TCGA-55-1595         TCGA-55-1596 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-64-1676         TCGA-64-1677         TCGA-64-1678 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-64-1680         TCGA-67-3770         TCGA-67-3771 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D34V3, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                185
  CLUS_2            3                211
  CLUS_3            1                 91
D34V4, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                 85
  CLUS_2            2                106
  CLUS_3            0                110
  CLUS_4            0                100
D34V5, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                 83
  CLUS_2            0                 75
  CLUS_3            1                 74
D34V6, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            1                 88
  CLUS_3            1                 64
  CLUS_4            1                 57
D34V7, multiclass
D34V8, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                156
  CLUS_2            2                103
  CLUS_3            2                126
D34V9, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                170
  CLUS_2            3                195
  CLUS_3            2                 96
D34V10, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                162
  CLUS_2            3                241
  CLUS_3            1                 58
D34V11, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                156
  CLUS_2            2                172
  CLUS_3            0                 73
D34V12, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                152
  CLUS_2            0                 46
  CLUS_3            2                203

Clustering(35) Variable = 19q gain
D35V1, multiclass
[1] "Remove cluster labels:" "19Q GAIN CNV"          
clus
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2665 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"19Q GAIN WILD-TYPE" 
D35V2, multiclass
[1] "Remove cluster labels:" "19Q GAIN CNV"          
clus
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2665 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"19Q GAIN WILD-TYPE" 
D35V3, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            7                180
  CLUS_2            5                209
  CLUS_3           12                 80
D35V4, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            4                 82
  CLUS_2           11                 97
  CLUS_3            4                106
  CLUS_4            2                 98
D35V5, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            2                 83
  CLUS_2            2                 73
  CLUS_3            6                 69
D35V6, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            2                 21
  CLUS_2            0                 89
  CLUS_3            6                 59
  CLUS_4            2                 56
D35V7, multiclass
D35V8, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            5                153
  CLUS_2            3                102
  CLUS_3           13                115
D35V9, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            4                167
  CLUS_2           14                184
  CLUS_3            5                 93
D35V10, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            4                160
  CLUS_2           18                226
  CLUS_3            1                 58
D35V11, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            4                153
  CLUS_2           14                160
  CLUS_3            3                 70
D35V12, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            5                148
  CLUS_2            1                 45
  CLUS_3           15                190

Clustering(36) Variable = 20p gain
D36V1, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            1                  8
  CLUS_3            0                 12
  CLUS_4            3                  3
D36V2, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            3                  4
  CLUS_2            0                 13
  CLUS_3            1                 11
D36V3, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           24                163
  CLUS_2           13                201
  CLUS_3           26                 66
D36V4, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            7                 79
  CLUS_2           31                 77
  CLUS_3           10                100
  CLUS_4            5                 95
D36V5, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            9                 76
  CLUS_2            7                 68
  CLUS_3           18                 57
D36V6, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            2                 21
  CLUS_2           13                 76
  CLUS_3           12                 53
  CLUS_4            7                 51
D36V7, multiclass
D36V8, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           15                143
  CLUS_2            8                 97
  CLUS_3           32                 96
D36V9, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           13                158
  CLUS_2           34                164
  CLUS_3           14                 84
D36V10, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           11                153
  CLUS_2           40                204
  CLUS_3           10                 49
D36V11, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           12                145
  CLUS_2           31                143
  CLUS_3           11                 62
D36V12, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           13                140
  CLUS_2            7                 39
  CLUS_3           34                171

Clustering(37) Variable = 20q gain
D37V1, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            1                  8
  CLUS_3            0                 12
  CLUS_4            4                  2
D37V2, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            4                  3
  CLUS_2            0                 13
  CLUS_3            1                 11
D37V3, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           37                150
  CLUS_2           14                200
  CLUS_3           27                 65
D37V4, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            7                 79
  CLUS_2           39                 69
  CLUS_3           12                 98
  CLUS_4            6                 94
D37V5, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           10                 75
  CLUS_2            9                 66
  CLUS_3           25                 50
D37V6, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            3                 20
  CLUS_2           17                 72
  CLUS_3           18                 47
  CLUS_4            6                 52
D37V7, multiclass
D37V8, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           19                139
  CLUS_2           11                 94
  CLUS_3           39                 89
D37V9, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           16                155
  CLUS_2           45                153
  CLUS_3           14                 84
D37V10, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           14                150
  CLUS_2           51                193
  CLUS_3           10                 49
D37V11, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           16                141
  CLUS_2           39                135
  CLUS_3           10                 63
D37V12, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           15                138
  CLUS_2            6                 40
  CLUS_3           44                161

Clustering(38) Variable = 21q gain
D38V1, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            0                  9
  CLUS_3            1                 11
  CLUS_4            2                  4
D38V2, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            1                 12
  CLUS_3            0                 12
D38V3, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           29                158
  CLUS_2            9                205
  CLUS_3            5                 87
D38V4, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            7                 79
  CLUS_2           13                 95
  CLUS_3           14                 96
  CLUS_4            1                 99
D38V5, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           12                 73
  CLUS_2            3                 72
  CLUS_3            7                 68
D38V6, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            2                 21
  CLUS_2           13                 76
  CLUS_3            6                 59
  CLUS_4            1                 57
D38V7, multiclass
D38V8, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           15                143
  CLUS_2           13                 92
  CLUS_3            7                121
D38V9, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            9                162
  CLUS_2           24                174
  CLUS_3            7                 91
D38V10, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           10                154
  CLUS_2           24                220
  CLUS_3            6                 53
D38V11, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           12                145
  CLUS_2           18                156
  CLUS_3            5                 68
D38V12, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           11                142
  CLUS_2            5                 41
  CLUS_3           19                186

Clustering(39) Variable = 22q gain
D39V1, multiclass
[1] "Remove cluster labels:" "22Q GAIN CNV"          
clus
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1594         TCGA-55-1595 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"22Q GAIN WILD-TYPE" 
D39V2, multiclass
[1] "Remove cluster labels:" "22Q GAIN CNV"          
clus
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1594         TCGA-55-1595 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-67-3774 
"22Q GAIN WILD-TYPE" 
D39V3, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1           11                176
  CLUS_2            2                212
  CLUS_3            7                 85
D39V4, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            4                 82
  CLUS_2            8                100
  CLUS_3            1                109
  CLUS_4            3                 97
D39V5, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            4                 81
  CLUS_2            2                 73
  CLUS_3            4                 71
D39V6, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            2                 21
  CLUS_2            2                 87
  CLUS_3            5                 60
  CLUS_4            1                 57
D39V7, multiclass
D39V8, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            5                153
  CLUS_2            6                 99
  CLUS_3            8                120
D39V9, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            3                168
  CLUS_2           11                187
  CLUS_3            6                 92
D39V10, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            3                161
  CLUS_2           12                232
  CLUS_3            5                 54
D39V11, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            3                154
  CLUS_2            7                167
  CLUS_3            6                 67
D39V12, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            5                148
  CLUS_2            4                 42
  CLUS_3            7                198

Clustering(40) Variable = Xq gain
D40V1, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           1                 4
  CLUS_2           1                 8
  CLUS_3           1                11
  CLUS_4           0                 6
D40V2, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           0                 7
  CLUS_2           1                12
  CLUS_3           2                10
D40V3, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1          13               174
  CLUS_2           0               214
  CLUS_3           4                88
D40V4, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           1                85
  CLUS_2           5               103
  CLUS_3           5               105
  CLUS_4           2                98
D40V5, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           2                83
  CLUS_2           3                72
  CLUS_3           4                71
D40V6, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           0                23
  CLUS_2           6                83
  CLUS_3           1                64
  CLUS_4           2                56
D40V7, multiclass
D40V8, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           5               153
  CLUS_2           7                98
  CLUS_3           5               123
D40V9, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           4               167
  CLUS_2           8               190
  CLUS_3           5                93
D40V10, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           4               160
  CLUS_2          10               234
  CLUS_3           3                56
D40V11, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           2               155
  CLUS_2           7               167
  CLUS_3           4                69
D40V12, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           3               150
  CLUS_2           3                43
  CLUS_3           7               198

Clustering(41) Variable = 1p loss
D41V1, multiclass
[1] "Remove cluster labels:" "1P LOSS CNV"           
clus
      1P LOSS CNV 1P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-35-3615        TCGA-35-4122 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-35-4123        TCGA-44-2655        TCGA-44-2656        TCGA-44-2657 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-2659        TCGA-44-2661        TCGA-44-2662        TCGA-44-2665 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-2666        TCGA-44-2668        TCGA-44-3398        TCGA-44-3918 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-55-1592        TCGA-55-1594 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D41V2, multiclass
[1] "Remove cluster labels:" "1P LOSS CNV"           
clus
      1P LOSS CNV 1P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-35-3615        TCGA-35-4122 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-35-4123        TCGA-44-2655        TCGA-44-2656        TCGA-44-2657 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-2659        TCGA-44-2661        TCGA-44-2662        TCGA-44-2665 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-2666        TCGA-44-2668        TCGA-44-3398        TCGA-44-3918 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-55-1592        TCGA-55-1594 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D41V3, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           6               181
  CLUS_2           7               207
  CLUS_3          16                76
D41V4, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           5                81
  CLUS_2          16                92
  CLUS_3           3               107
  CLUS_4           1                99
D41V5, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           4                81
  CLUS_2           4                71
  CLUS_3          10                65
D41V6, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1                22
  CLUS_2           4                85
  CLUS_3           9                56
  CLUS_4           4                54
D41V7, multiclass
D41V8, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           8               150
  CLUS_2           5               100
  CLUS_3          13               115
D41V9, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1          11               160
  CLUS_2          12               186
  CLUS_3           4                94
D41V10, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           7               157
  CLUS_2          19               225
  CLUS_3           1                58
D41V11, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           9               148
  CLUS_2          14               160
  CLUS_3           2                71
D41V12, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           7               146
  CLUS_2           3                43
  CLUS_3          15               190

Clustering(42) Variable = 1q loss
D42V1, multiclass
D42V2, multiclass
D42V3, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           1               186
  CLUS_2           2               212
  CLUS_3           7                85
D42V4, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           1                85
  CLUS_2           6               102
  CLUS_3           1               109
  CLUS_4           1                99
D42V5, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2                83
  CLUS_2           1                74
  CLUS_3           5                70
D42V6, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           1                22
  CLUS_2           1                88
  CLUS_3           6                59
  CLUS_4           0                58
D42V7, multiclass
D42V8, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2               156
  CLUS_2           2               103
  CLUS_3           6               122
D42V9, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2               169
  CLUS_2           5               193
  CLUS_3           3                95
D42V10, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           1               163
  CLUS_2           8               236
  CLUS_3           1                58
D42V11, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2               155
  CLUS_2           6               168
  CLUS_3           1                72
D42V12, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           1               152
  CLUS_2           2                44
  CLUS_3           6               199

Clustering(43) Variable = 2p loss
D43V1, multiclass
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-2666        TCGA-44-2668        TCGA-44-3398        TCGA-44-3918 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-55-1592        TCGA-55-1594 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D43V2, multiclass
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-2666        TCGA-44-2668        TCGA-44-3398        TCGA-44-3918 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-55-1592        TCGA-55-1594 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-55-1595        TCGA-55-1596        TCGA-64-1676        TCGA-64-1677 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D43V3, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           3               184
  CLUS_2           2               212
  CLUS_3           1                91
D43V4, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2                84
  CLUS_2           1               107
  CLUS_3           2               108
  CLUS_4           0               100
D43V5, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1                84
  CLUS_2           1                74
  CLUS_3           1                74
D43V6, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                23
  CLUS_2           1                88
  CLUS_3           2                63
  CLUS_4           0                58
D43V7, multiclass
D43V8, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2               156
  CLUS_2           1               104
  CLUS_3           2               126
D43V9, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2               169
  CLUS_2           2               196
  CLUS_3           2                96
D43V10, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2               162
  CLUS_2           3               241
  CLUS_3           1                58
D43V11, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2               155
  CLUS_2           3               171
  CLUS_3           0                73
D43V12, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2               151
  CLUS_2           0                46
  CLUS_3           3               202

Clustering(44) Variable = 2q loss
D44V1, multiclass
D44V2, multiclass
D44V3, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           4               183
  CLUS_2           0               214
  CLUS_3           0                92
D44V4, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           2                84
  CLUS_2           0               108
  CLUS_3           2               108
  CLUS_4           0               100
D44V5, multiclass
[1] "Remove cluster labels:" "2Q LOSS CNV"           
clus
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                2               233 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-05-4384 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4396        TCGA-05-4397        TCGA-05-4398        TCGA-05-4402 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4405        TCGA-05-4410        TCGA-05-4417        TCGA-05-4418 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4420        TCGA-05-4422        TCGA-05-4426        TCGA-05-4427 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4430        TCGA-05-4434        TCGA-05-5420        TCGA-05-5423 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-5425        TCGA-05-5429        TCGA-05-5715        TCGA-35-3615 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-38-4625 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-38-4626        TCGA-38-4627        TCGA-38-4629        TCGA-38-6178 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2656        TCGA-44-2657        TCGA-44-2661        TCGA-44-2665 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2668        TCGA-44-3396        TCGA-44-3398        TCGA-44-3918 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-44-5643        TCGA-44-5644 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-5645        TCGA-44-6144        TCGA-44-6145        TCGA-44-6146 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-6147        TCGA-44-6148        TCGA-44-6774        TCGA-44-6775 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-6776        TCGA-44-6777        TCGA-44-6778        TCGA-44-6779 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7659        TCGA-44-7660        TCGA-44-7661        TCGA-44-7662 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7667        TCGA-44-7669        TCGA-44-7670        TCGA-44-7671 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7672        TCGA-49-4486        TCGA-49-4487        TCGA-49-4488 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4494        TCGA-49-4501        TCGA-49-4505        TCGA-49-4506 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4507        TCGA-49-4510        TCGA-49-4512        TCGA-49-4514 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-6742        TCGA-49-6743        TCGA-49-6744        TCGA-49-6745 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-6761        TCGA-49-6767        TCGA-50-5044        TCGA-50-5045 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5049        TCGA-50-5051        TCGA-50-5066        TCGA-50-5068 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5072        TCGA-50-5930        TCGA-50-5931        TCGA-50-5932 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5933        TCGA-50-5936        TCGA-50-5939        TCGA-50-5941 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5942        TCGA-50-5944        TCGA-50-5946        TCGA-50-6590 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-6591        TCGA-50-6592        TCGA-50-6593        TCGA-50-6594 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-6595        TCGA-50-6597        TCGA-50-6673        TCGA-50-7109 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-53-7624        TCGA-53-7626        TCGA-53-7813        TCGA-55-1592 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1596        TCGA-55-5899        TCGA-55-6543 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6712        TCGA-55-6969        TCGA-55-6970        TCGA-55-6971 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6978        TCGA-55-6979        TCGA-55-6981        TCGA-55-6982 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7573        TCGA-55-7574        TCGA-55-7728        TCGA-55-7815 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7910        TCGA-55-7911        TCGA-64-1676        TCGA-64-1677 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1679        TCGA-64-1680        TCGA-64-1681 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-5774        TCGA-64-5778        TCGA-64-5779        TCGA-64-5781 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-5815        TCGA-67-3771        TCGA-67-6215        TCGA-67-6216 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-67-6217        TCGA-69-7761        TCGA-69-7763        TCGA-69-7764 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-69-7765        TCGA-71-6725        TCGA-73-4658        TCGA-73-4659 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-4670        TCGA-73-4675        TCGA-73-4676        TCGA-73-7498 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-7499        TCGA-75-5122        TCGA-75-5125        TCGA-75-6203 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-6205        TCGA-75-6206        TCGA-75-6207        TCGA-75-6212 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-6214        TCGA-75-7027        TCGA-75-7030        TCGA-75-7031 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7143        TCGA-78-7145        TCGA-78-7146        TCGA-78-7147 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7148        TCGA-78-7149        TCGA-78-7150        TCGA-78-7152 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7153        TCGA-78-7154        TCGA-78-7155        TCGA-78-7156 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7158        TCGA-78-7159        TCGA-78-7160        TCGA-78-7161 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7162        TCGA-78-7163        TCGA-78-7166        TCGA-78-7167 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7535        TCGA-78-7536        TCGA-78-7537        TCGA-78-7539 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7540        TCGA-78-7542        TCGA-78-7633        TCGA-80-5607 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-80-5608        TCGA-80-5611        TCGA-83-5908        TCGA-86-6562 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-6851        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-7953        TCGA-86-7954        TCGA-86-7955        TCGA-91-6828 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6829        TCGA-91-6830        TCGA-91-6831        TCGA-91-6835 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6836        TCGA-91-6840        TCGA-91-6847        TCGA-91-6848 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6849        TCGA-91-7771        TCGA-93-7348        TCGA-95-7039 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-95-7043        TCGA-95-7567        TCGA-95-7944        TCGA-95-7947 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-95-7948        TCGA-97-7546        TCGA-97-7552        TCGA-97-7553 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-97-7554        TCGA-97-7937        TCGA-97-7938        TCGA-97-7941 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-99-7458 
"2Q LOSS WILD-TYPE" 
D44V6, multiclass
[1] "Remove cluster labels:" "2Q LOSS CNV"           
clus
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                2               233 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-05-4384 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4396        TCGA-05-4397        TCGA-05-4398        TCGA-05-4402 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4405        TCGA-05-4410        TCGA-05-4417        TCGA-05-4418 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4420        TCGA-05-4422        TCGA-05-4426        TCGA-05-4427 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-4430        TCGA-05-4434        TCGA-05-5420        TCGA-05-5423 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-05-5425        TCGA-05-5429        TCGA-05-5715        TCGA-35-3615 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-35-5375        TCGA-38-4625 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-38-4626        TCGA-38-4627        TCGA-38-4629        TCGA-38-6178 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2656        TCGA-44-2657        TCGA-44-2661        TCGA-44-2665 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-2668        TCGA-44-3396        TCGA-44-3398        TCGA-44-3918 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-3919        TCGA-44-4112        TCGA-44-5643        TCGA-44-5644 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-5645        TCGA-44-6144        TCGA-44-6145        TCGA-44-6146 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-6147        TCGA-44-6148        TCGA-44-6774        TCGA-44-6775 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-6776        TCGA-44-6777        TCGA-44-6778        TCGA-44-6779 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7659        TCGA-44-7660        TCGA-44-7661        TCGA-44-7662 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7667        TCGA-44-7669        TCGA-44-7670        TCGA-44-7671 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-44-7672        TCGA-49-4486        TCGA-49-4487        TCGA-49-4488 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4494        TCGA-49-4501        TCGA-49-4505        TCGA-49-4506 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-4507        TCGA-49-4510        TCGA-49-4512        TCGA-49-4514 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-6742        TCGA-49-6743        TCGA-49-6744        TCGA-49-6745 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-49-6761        TCGA-49-6767        TCGA-50-5044        TCGA-50-5045 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5049        TCGA-50-5051        TCGA-50-5066        TCGA-50-5068 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5072        TCGA-50-5930        TCGA-50-5931        TCGA-50-5932 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5933        TCGA-50-5936        TCGA-50-5939        TCGA-50-5941 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-5942        TCGA-50-5944        TCGA-50-5946        TCGA-50-6590 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-6591        TCGA-50-6592        TCGA-50-6593        TCGA-50-6594 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-50-6595        TCGA-50-6597        TCGA-50-6673        TCGA-50-7109 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-53-7624        TCGA-53-7626        TCGA-53-7813        TCGA-55-1592 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1596        TCGA-55-5899        TCGA-55-6543 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6712        TCGA-55-6969        TCGA-55-6970        TCGA-55-6971 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-6978        TCGA-55-6979        TCGA-55-6981        TCGA-55-6982 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7573        TCGA-55-7574        TCGA-55-7728        TCGA-55-7815 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-55-7910        TCGA-55-7911        TCGA-64-1676        TCGA-64-1677 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1679        TCGA-64-1680        TCGA-64-1681 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-5774        TCGA-64-5778        TCGA-64-5779        TCGA-64-5781 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-64-5815        TCGA-67-3771        TCGA-67-6215        TCGA-67-6216 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-67-6217        TCGA-69-7761        TCGA-69-7763        TCGA-69-7764 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-69-7765        TCGA-71-6725        TCGA-73-4658        TCGA-73-4659 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-4670        TCGA-73-4675        TCGA-73-4676        TCGA-73-7498 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-73-7499        TCGA-75-5122        TCGA-75-5125        TCGA-75-6203 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-6205        TCGA-75-6206        TCGA-75-6207        TCGA-75-6212 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-75-6214        TCGA-75-7027        TCGA-75-7030        TCGA-75-7031 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7143        TCGA-78-7145        TCGA-78-7146        TCGA-78-7147 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7148        TCGA-78-7149        TCGA-78-7150        TCGA-78-7152 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7153        TCGA-78-7154        TCGA-78-7155        TCGA-78-7156 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7158        TCGA-78-7159        TCGA-78-7160        TCGA-78-7161 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7162        TCGA-78-7163        TCGA-78-7166        TCGA-78-7167 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7535        TCGA-78-7536        TCGA-78-7537        TCGA-78-7539 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-78-7540        TCGA-78-7542        TCGA-78-7633        TCGA-80-5607 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-80-5608        TCGA-80-5611        TCGA-83-5908        TCGA-86-6562 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-6851        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-86-7953        TCGA-86-7954        TCGA-86-7955        TCGA-91-6828 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6829        TCGA-91-6830        TCGA-91-6831        TCGA-91-6835 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6836        TCGA-91-6840        TCGA-91-6847        TCGA-91-6848 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-91-6849        TCGA-91-7771        TCGA-93-7348        TCGA-95-7039 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-95-7043        TCGA-95-7567        TCGA-95-7944        TCGA-95-7947 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-95-7948        TCGA-97-7546        TCGA-97-7552        TCGA-97-7553 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-97-7554        TCGA-97-7937        TCGA-97-7938        TCGA-97-7941 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-99-7458 
"2Q LOSS WILD-TYPE" 
D44V7, multiclass
D44V8, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               157
  CLUS_2           1               104
  CLUS_3           1               127
D44V9, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               170
  CLUS_2           3               195
  CLUS_3           0                98
D44V10, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               163
  CLUS_2           3               241
  CLUS_3           0                59
D44V11, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               156
  CLUS_2           2               172
  CLUS_3           1                72
D44V12, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               152
  CLUS_2           0                46
  CLUS_3           3               202

Clustering(45) Variable = 3p loss
D45V1, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           1                 8
  CLUS_3           2                10
  CLUS_4           3                 3
D45V2, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           2                11
  CLUS_3           1                11
D45V3, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          45               142
  CLUS_2          21               193
  CLUS_3          30                62
D45V4, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          14                72
  CLUS_2          37                71
  CLUS_3          23                87
  CLUS_4           6                94
D45V5, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          13                72
  CLUS_2          11                64
  CLUS_3          20                55
D45V6, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           4                19
  CLUS_2          19                70
  CLUS_3          15                50
  CLUS_4           6                52
D45V7, multiclass
D45V8, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          23               135
  CLUS_2          19                86
  CLUS_3          34                94
D45V9, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          23               148
  CLUS_2          48               150
  CLUS_3          17                81
D45V10, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          22               142
  CLUS_2          58               186
  CLUS_3           8                51
D45V11, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          24               133
  CLUS_2          47               127
  CLUS_3           8                65
D45V12, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          23               130
  CLUS_2          10                36
  CLUS_3          46               159

Clustering(46) Variable = 3q loss
D46V1, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           0                 9
  CLUS_3           2                10
  CLUS_4           1                 5
D46V2, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           2                11
  CLUS_3           0                12
D46V3, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          30               157
  CLUS_2          11               203
  CLUS_3          15                77
D46V4, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          13                73
  CLUS_2          22                86
  CLUS_3          13                97
  CLUS_4           2                98
D46V5, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           5                80
  CLUS_2           9                66
  CLUS_3           9                66
D46V6, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           3                20
  CLUS_2           9                80
  CLUS_3           6                59
  CLUS_4           5                53
D46V7, multiclass
D46V8, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          19               139
  CLUS_2           9                96
  CLUS_3          16               112
D46V9, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          17               154
  CLUS_2          27               171
  CLUS_3           9                89
D46V10, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          14               150
  CLUS_2          36               208
  CLUS_3           3                56
D46V11, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          18               139
  CLUS_2          29               145
  CLUS_3           2                71
D46V12, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          14               139
  CLUS_2           6                40
  CLUS_3          29               176

Clustering(47) Variable = 4p loss
D47V1, multiclass
[1] "Remove cluster labels:" "4P LOSS CNV"           
clus
      4P LOSS CNV 4P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-64-1676        TCGA-64-1677 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D47V2, multiclass
[1] "Remove cluster labels:" "4P LOSS CNV"           
clus
      4P LOSS CNV 4P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-64-1676        TCGA-64-1677 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D47V3, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          19               168
  CLUS_2           5               209
  CLUS_3          16                76
D47V4, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           3                83
  CLUS_2          19                89
  CLUS_3           6               104
  CLUS_4           3                97
D47V5, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           8                77
  CLUS_2           5                70
  CLUS_3          12                63
D47V6, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           2                21
  CLUS_2           6                83
  CLUS_3          11                54
  CLUS_4           6                52
D47V7, multiclass
D47V8, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           4               154
  CLUS_2           7                98
  CLUS_3          22               106
D47V9, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           7               164
  CLUS_2          28               170
  CLUS_3           2                96
D47V10, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           8               156
  CLUS_2          28               216
  CLUS_3           1                58
D47V11, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           9               148
  CLUS_2          21               153
  CLUS_3           1                72
D47V12, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          10               143
  CLUS_2           0                46
  CLUS_3          21               184

Clustering(48) Variable = 4q loss
D48V1, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           0                 9
  CLUS_3           0                12
  CLUS_4           3                 3
D48V2, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           0                13
  CLUS_3           0                12
D48V3, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          24               163
  CLUS_2           2               212
  CLUS_3          21                71
D48V4, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           3                83
  CLUS_2          24                84
  CLUS_3           5               105
  CLUS_4           4                96
D48V5, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           9                76
  CLUS_2           7                68
  CLUS_3          12                63
D48V6, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                21
  CLUS_2           9                80
  CLUS_3          11                54
  CLUS_4           6                52
D48V7, multiclass
D48V8, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           5               153
  CLUS_2           5               100
  CLUS_3          29                99
D48V9, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           7               164
  CLUS_2          31               167
  CLUS_3           6                92
D48V10, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           7               157
  CLUS_2          35               209
  CLUS_3           2                57
D48V11, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          10               147
  CLUS_2          24               150
  CLUS_3           2                71
D48V12, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           9               144
  CLUS_2           0                46
  CLUS_3          27               178

Clustering(49) Variable = 5p loss
D49V1, multiclass
[1] "Remove cluster labels:" "5P LOSS CNV"           
clus
      5P LOSS CNV 5P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-64-1676        TCGA-64-1677 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
D49V2, multiclass
[1] "Remove cluster labels:" "5P LOSS CNV"           
clus
      5P LOSS CNV 5P LOSS WILD-TYPE 
                1                31 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1592 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-55-1594        TCGA-55-1595        TCGA-64-1676        TCGA-64-1677 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-64-1678        TCGA-64-1680        TCGA-67-3770        TCGA-67-3771 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-67-3772        TCGA-67-3773        TCGA-67-3774 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
D49V3, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           6               181
  CLUS_2           1               213
  CLUS_3           4                88
D49V4, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0                86
  CLUS_2           5               103
  CLUS_3           3               107
  CLUS_4           1                99
D49V5, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1                84
  CLUS_2           1                74
  CLUS_3           2                73
D49V6, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0                23
  CLUS_2           1                88
  CLUS_3           2                63
  CLUS_4           1                57
D49V7, multiclass
D49V8, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1               157
  CLUS_2           1               104
  CLUS_3           8               120
D49V9, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0               171
  CLUS_2           8               190
  CLUS_3           2                96
D49V10, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0               164
  CLUS_2           8               236
  CLUS_3           2                57
D49V11, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0               157
  CLUS_2           7               167
  CLUS_3           1                72
D49V12, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0               153
  CLUS_2           1                45
  CLUS_3           7               198

Clustering(50) Variable = 5q loss
D50V1, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           1                 8
  CLUS_3           0                12
  CLUS_4           3                 3
D50V2, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           0                13
  CLUS_3           1                11
D50V3, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          31               156
  CLUS_2           9               205
  CLUS_3          20                72
D50V4, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           6                80
  CLUS_2          24                84
  CLUS_3          15                95
  CLUS_4           3                97
D50V5, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          11                74
  CLUS_2           6                69
  CLUS_3          17                58
D50V6, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           4                19
  CLUS_2          10                79
  CLUS_3          15                50
  CLUS_4           5                53
D50V7, multiclass
D50V8, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          13               145
  CLUS_2          14                91
  CLUS_3          23               105
D50V9, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          12               159
  CLUS_2          32               166
  CLUS_3          10                88
D50V10, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          10               154
  CLUS_2          38               206
  CLUS_3           6                53
D50V11, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          13               144
  CLUS_2          29               145
  CLUS_3           5                68
D50V12, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          11               142
  CLUS_2           4                42
  CLUS_3          32               173

Clustering(51) Variable = 6p loss
D51V1, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1                 4
  CLUS_2           1                 8
  CLUS_3           0                12
  CLUS_4           1                 5
D51V2, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           0                13
  CLUS_3           2                10
D51V3, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          23               164
  CLUS_2           8               206
  CLUS_3          12                80
D51V4, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           8                78
  CLUS_2          10                98
  CLUS_3          13                97
  CLUS_4           2                98
D51V5, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           6                79
  CLUS_2           3                72
  CLUS_3          10                65
D51V6, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           2                21
  CLUS_2           5                84
  CLUS_3           8                57
  CLUS_4           4                54
D51V7, multiclass
D51V8, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          13               145
  CLUS_2          10                95
  CLUS_3          10               118
D51V9, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          14               157
  CLUS_2          20               178
  CLUS_3           5                93
D51V10, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          13               151
  CLUS_2          23               221
  CLUS_3           3                56
D51V11, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          15               142
  CLUS_2          16               158
  CLUS_3           2                71
D51V12, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          12               141
  CLUS_2           7                39
  CLUS_3          14               191

Clustering(52) Variable = 6q loss
D52V1, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           1                 4
  CLUS_2           1                 8
  CLUS_3           2                10
  CLUS_4           2                 4
D52V2, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           2                 5
  CLUS_2           2                11
  CLUS_3           2                10
D52V3, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          46               141
  CLUS_2          38               176
  CLUS_3          28                64
D52V4, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          28                58
  CLUS_2          27                81
  CLUS_3          33                77
  CLUS_4           4                96
D52V5, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          12                73
  CLUS_2          15                60
  CLUS_3          20                55
D52V6, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1           2                21
  CLUS_2          12                77
  CLUS_3          16                49
  CLUS_4          17                41
D52V7, multiclass
D52V8, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          43               115
  CLUS_2          21                84
  CLUS_3          24               104
D52V9, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          41               130
  CLUS_2          45               153
  CLUS_3          17                81
D52V10, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          37               127
  CLUS_2          52               192
  CLUS_3          14                45
D52V11, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          37               120
  CLUS_2          44               130
  CLUS_3          12                61
D52V12, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          36               117
  CLUS_2          18                28
  CLUS_3          39               166

Clustering(53) Variable = 7p loss
D53V1, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           0                 9
  CLUS_3           2                10
  CLUS_4           1                 5
D53V2, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1                 6
  CLUS_2           2                11
  CLUS_3           0                12
D53V3, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           2               185
  CLUS_2           5               209
  CLUS_3           7                85
D53V4, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           2                84
  CLUS_2           5               103
  CLUS_3           2               108
  CLUS_4           1                99
D53V5, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1                84
  CLUS_2           2                73
  CLUS_3           3                72
D53V6, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           0                23
  CLUS_2           2                87
  CLUS_3           2                63
  CLUS_4           2                56
D53V7, multiclass
D53V8, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           6               152
  CLUS_2           0               105
  CLUS_3           6               122
D53V9, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           7               164
  CLUS_2           7               191
  CLUS_3           0                98
D53V10, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           6               158
  CLUS_2           7               237
  CLUS_3           1                58
D53V11, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           4               153
  CLUS_2           5               169
  CLUS_3           1                72
D53V12, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           3               150
  CLUS_2           1                45
  CLUS_3           6               199

Clustering(54) Variable = 7q loss
D54V1, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           1                 4
  CLUS_2           0                 9
  CLUS_3           2                10
  CLUS_4           1                 5
D54V2, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           2                 5
  CLUS_2           2                11
  CLUS_3           0                12
D54V3, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           5               182
  CLUS_2           8               206
  CLUS_3           4                88
D54V4, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           3                83
  CLUS_2           5               103
  CLUS_3           3               107
  CLUS_4           1                99
D54V5, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           2                83
  CLUS_2           1                74
  CLUS_3           3                72
D54V6, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           1                22
  CLUS_2           2                87
  CLUS_3           2                63
  CLUS_4           1                57
D54V7, multiclass
D54V8, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           5               153
  CLUS_2           1               104
  CLUS_3           6               122
D54V9, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           6               165
  CLUS_2           8               190
  CLUS_3           3                95
D54V10, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           6               158
  CLUS_2           8               236
  CLUS_3           3                56
D54V11, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           3               154
  CLUS_2           5               169
  CLUS_3           4                69
D54V12, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           3               150
  CLUS_2           3                43
  CLUS_3           6               199

Clustering(55) Variable = 8p loss
D55V1, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           4                 1
  CLUS_2           3                 6
  CLUS_3           2                10
  CLUS_4           2                 4
D55V2, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           2                11
  CLUS_3           6                 6
D55V3, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          89                98
  CLUS_2          16               198
  CLUS_3          17                75
D55V4, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          15                71
  CLUS_2          34                74
  CLUS_3          38                72
  CLUS_4          11                89
D55V5, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          23                62
  CLUS_2          15                60
  CLUS_3          24                51
D55V6, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           9                14
  CLUS_2          22                67
  CLUS_3          22                43
  CLUS_4           9                49
D55V7, multiclass
D55V8, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          34               124
  CLUS_2          41                64
  CLUS_3          26               102
D55V9, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          31               140
  CLUS_2          61               137
  CLUS_3          24                74
D55V10, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          33               131
  CLUS_2          74               170
  CLUS_3           9                50
D55V11, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          28               129
  CLUS_2          55               119
  CLUS_3          15                58
D55V12, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          28               125
  CLUS_2          11                35
  CLUS_3          59               146

Clustering(56) Variable = 8q loss
D56V1, multiclass
D56V2, multiclass
D56V3, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1          17               170
  CLUS_2           3               211
  CLUS_3           1                91
D56V4, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           4                82
  CLUS_2           3               105
  CLUS_3           7               103
  CLUS_4           4                96
D56V5, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           8                77
  CLUS_2           0                75
  CLUS_3           1                74
D56V6, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           3                20
  CLUS_2           5                84
  CLUS_3           1                64
  CLUS_4           0                58
D56V7, multiclass
D56V8, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           6               152
  CLUS_2           9                96
  CLUS_3           1               127
D56V9, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           6               165
  CLUS_2           8               190
  CLUS_3           6                92
D56V10, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           5               159
  CLUS_2          12               232
  CLUS_3           3                56
D56V11, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           6               151
  CLUS_2           7               167
  CLUS_3           5                68
D56V12, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           6               147
  CLUS_2           5                41
  CLUS_3           7               198

Clustering(57) Variable = 9p loss
D57V1, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           1                 8
  CLUS_3           4                 8
  CLUS_4           4                 2
D57V2, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           4                 3
  CLUS_2           4                 9
  CLUS_3           1                11
D57V3, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          73               114
  CLUS_2          41               173
  CLUS_3          28                64
D57V4, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          26                60
  CLUS_2          48                60
  CLUS_3          31                79
  CLUS_4          13                87
D57V5, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          22                63
  CLUS_2          22                53
  CLUS_3          28                47
D57V6, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1           3                20
  CLUS_2          22                67
  CLUS_3          26                39
  CLUS_4          21                37
D57V7, multiclass
D57V8, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          42               116
  CLUS_2          24                81
  CLUS_3          50                78
D57V9, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          47               124
  CLUS_2          60               138
  CLUS_3          27                71
D57V10, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          45               119
  CLUS_2          74               170
  CLUS_3          15                44
D57V11, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          43               114
  CLUS_2          50               124
  CLUS_3          24                49
D57V12, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          41               112
  CLUS_2          14                32
  CLUS_3          62               143

Clustering(58) Variable = 9q loss
D58V1, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           0                 5
  CLUS_2           1                 8
  CLUS_3           4                 8
  CLUS_4           3                 3
D58V2, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           3                 4
  CLUS_2           4                 9
  CLUS_3           1                11
D58V3, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          60               127
  CLUS_2          28               186
  CLUS_3          32                60
D58V4, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          19                67
  CLUS_2          47                61
  CLUS_3          20                90
  CLUS_4           9                91
D58V5, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          19                66
  CLUS_2          15                60
  CLUS_3          22                53
D58V6, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1           2                21
  CLUS_2          21                68
  CLUS_3          20                45
  CLUS_4          13                45
D58V7, multiclass
D58V8, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          30               128
  CLUS_2          22                83
  CLUS_3          43                85
D58V9, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          33               138
  CLUS_2          56               142
  CLUS_3          22                76
D58V10, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          33               131
  CLUS_2          66               178
  CLUS_3          12                47
D58V11, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          29               128
  CLUS_2          45               129
  CLUS_3          20                53
D58V12, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          30               123
  CLUS_2          13                33
  CLUS_3          51               154

Clustering(59) Variable = 10p loss
D59V1, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            1                  8
  CLUS_3            1                 11
  CLUS_4            1                  5
D59V2, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            1                 12
  CLUS_3            2                 10
D59V3, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           24                163
  CLUS_2            4                210
  CLUS_3           10                 82
D59V4, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            4                 82
  CLUS_2           15                 93
  CLUS_3           10                100
  CLUS_4            2                 98
D59V5, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            7                 78
  CLUS_2            2                 73
  CLUS_3           10                 65
D59V6, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            1                 22
  CLUS_2           11                 78
  CLUS_3            6                 59
  CLUS_4            1                 57
D59V7, multiclass
D59V8, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           10                148
  CLUS_2            8                 97
  CLUS_3           13                115
D59V9, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            7                164
  CLUS_2           16                182
  CLUS_3           12                 86
D59V10, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            6                158
  CLUS_2           20                224
  CLUS_3            9                 50
D59V11, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            4                153
  CLUS_2           15                159
  CLUS_3           12                 61
D59V12, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            4                149
  CLUS_2           10                 36
  CLUS_3           17                188

Clustering(60) Variable = 10q loss
D60V1, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            1                  8
  CLUS_3            1                 11
  CLUS_4            0                  6
D60V2, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            1                 12
  CLUS_3            2                 10
D60V3, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           26                161
  CLUS_2            9                205
  CLUS_3           14                 78
D60V4, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            7                 79
  CLUS_2           17                 91
  CLUS_3           13                 97
  CLUS_4            1                 99
D60V5, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            9                 76
  CLUS_2            2                 73
  CLUS_3           12                 63
D60V6, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            2                 21
  CLUS_2           12                 77
  CLUS_3            8                 57
  CLUS_4            1                 57
D60V7, multiclass
D60V8, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           13                145
  CLUS_2           10                 95
  CLUS_3           15                113
D60V9, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           13                158
  CLUS_2           17                181
  CLUS_3           13                 85
D60V10, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            9                155
  CLUS_2           24                220
  CLUS_3           10                 49
D60V11, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           10                147
  CLUS_2           17                157
  CLUS_3           11                 62
D60V12, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            7                146
  CLUS_2            9                 37
  CLUS_3           22                183

Clustering(61) Variable = 11p loss
D61V1, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            1                  8
  CLUS_3            0                 12
  CLUS_4            1                  5
D61V2, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            0                 13
  CLUS_3            1                 11
D61V3, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           22                165
  CLUS_2            5                209
  CLUS_3            9                 83
D61V4, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            6                 80
  CLUS_2            7                101
  CLUS_3           10                100
  CLUS_4            4                 96
D61V5, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            5                 80
  CLUS_2            2                 73
  CLUS_3           13                 62
D61V6, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            0                 23
  CLUS_2            7                 82
  CLUS_3           11                 54
  CLUS_4            2                 56
D61V7, multiclass
D61V8, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            5                153
  CLUS_2           12                 93
  CLUS_3           10                118
D61V9, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            7                164
  CLUS_2           20                178
  CLUS_3            6                 92
D61V10, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            6                158
  CLUS_2           24                220
  CLUS_3            3                 56
D61V11, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            5                152
  CLUS_2           19                155
  CLUS_3            3                 70
D61V12, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            6                147
  CLUS_2            5                 41
  CLUS_3           16                189

Clustering(62) Variable = 11q loss
D62V1, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            0                  9
  CLUS_3            1                 11
  CLUS_4            1                  5
D62V2, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            1                 12
  CLUS_3            0                 12
D62V3, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1           18                169
  CLUS_2            4                210
  CLUS_3            9                 83
D62V4, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            6                 80
  CLUS_2            6                102
  CLUS_3            8                102
  CLUS_4            3                 97
D62V5, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            2                 83
  CLUS_2            2                 73
  CLUS_3           10                 65
D62V6, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            2                 87
  CLUS_3            9                 56
  CLUS_4            2                 56
D62V7, multiclass
D62V8, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            7                151
  CLUS_2           10                 95
  CLUS_3            7                121
D62V9, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            9                162
  CLUS_2           17                181
  CLUS_3            4                 94
D62V10, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            9                155
  CLUS_2           18                226
  CLUS_3            3                 56
D62V11, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            7                150
  CLUS_2           13                161
  CLUS_3            3                 70
D62V12, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            7                146
  CLUS_2            4                 42
  CLUS_3           12                193

Clustering(63) Variable = 12p loss
D63V1, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            2                  7
  CLUS_3            1                 11
  CLUS_4            1                  5
D63V2, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            1                 12
  CLUS_3            2                 10
D63V3, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           17                170
  CLUS_2           15                199
  CLUS_3            8                 84
D63V4, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           13                 73
  CLUS_2            9                 99
  CLUS_3            9                101
  CLUS_4            1                 99
D63V5, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            8                 77
  CLUS_2            8                 67
  CLUS_3            6                 69
D63V6, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            1                 22
  CLUS_2           11                 78
  CLUS_3            4                 61
  CLUS_4            6                 52
D63V7, multiclass
D63V8, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           16                142
  CLUS_2            7                 98
  CLUS_3           10                118
D63V9, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           15                156
  CLUS_2           11                187
  CLUS_3           10                 88
D63V10, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           15                149
  CLUS_2           17                227
  CLUS_3            4                 55
D63V11, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           17                140
  CLUS_2           14                160
  CLUS_3            1                 72
D63V12, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           13                140
  CLUS_2            3                 43
  CLUS_3           16                189

Clustering(64) Variable = 12q loss
D64V1, multiclass
D64V2, multiclass
D64V3, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1           14                173
  CLUS_2            6                208
  CLUS_3            4                 88
D64V4, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            7                 79
  CLUS_2            5                103
  CLUS_3            7                103
  CLUS_4            3                 97
D64V5, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            6                 79
  CLUS_2            4                 71
  CLUS_3            4                 71
D64V6, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            2                 21
  CLUS_2            8                 81
  CLUS_3            2                 63
  CLUS_4            2                 56
D64V7, multiclass
D64V8, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            9                149
  CLUS_2            6                 99
  CLUS_3            6                122
D64V9, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            8                163
  CLUS_2            7                191
  CLUS_3            7                 91
D64V10, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            9                155
  CLUS_2           11                233
  CLUS_3            2                 57
D64V11, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1           12                145
  CLUS_2            9                165
  CLUS_3            1                 72
D64V12, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            9                144
  CLUS_2            2                 44
  CLUS_3           11                194

Clustering(65) Variable = 13q loss
D65V1, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            3                  2
  CLUS_2            2                  7
  CLUS_3            1                 11
  CLUS_4            2                  4
D65V2, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            3                  4
  CLUS_2            1                 12
  CLUS_3            4                  8
D65V3, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           76                111
  CLUS_2            4                210
  CLUS_3           35                 57
D65V4, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           17                 69
  CLUS_2           35                 73
  CLUS_3           27                 83
  CLUS_4            8                 92
D65V5, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           23                 62
  CLUS_2           13                 62
  CLUS_3           19                 56
D65V6, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1            2                 21
  CLUS_2           27                 62
  CLUS_3           19                 46
  CLUS_4            7                 51
D65V7, multiclass
D65V8, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           27                131
  CLUS_2           28                 77
  CLUS_3           34                 94
D65V9, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           28                143
  CLUS_2           60                138
  CLUS_3           19                 79
D65V10, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           27                137
  CLUS_2           66                178
  CLUS_3           14                 45
D65V11, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           27                130
  CLUS_2           47                127
  CLUS_3           14                 59
D65V12, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           25                128
  CLUS_2           14                 32
  CLUS_3           49                156

Clustering(66) Variable = 14q loss
D66V1, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            0                  9
  CLUS_3            2                 10
  CLUS_4            0                  6
D66V2, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            2                 11
  CLUS_3            0                 12
D66V3, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           23                164
  CLUS_2           12                202
  CLUS_3           12                 80
D66V4, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            6                 80
  CLUS_2           16                 92
  CLUS_3           11                 99
  CLUS_4            6                 94
D66V5, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            8                 77
  CLUS_2            2                 73
  CLUS_3           13                 62
D66V6, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            3                 20
  CLUS_2            4                 85
  CLUS_3           13                 52
  CLUS_4            3                 55
D66V7, multiclass
D66V8, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           13                145
  CLUS_2           12                 93
  CLUS_3           15                113
D66V9, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           11                160
  CLUS_2           27                171
  CLUS_3            7                 91
D66V10, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           13                151
  CLUS_2           29                215
  CLUS_3            3                 56
D66V11, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           14                143
  CLUS_2           24                150
  CLUS_3            2                 71
D66V12, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           13                140
  CLUS_2            4                 42
  CLUS_3           23                182

Clustering(67) Variable = 15q loss
D67V1, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            2                  3
  CLUS_2            2                  7
  CLUS_3            2                 10
  CLUS_4            0                  6
D67V2, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            2                 11
  CLUS_3            4                  8
D67V3, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           54                133
  CLUS_2           11                203
  CLUS_3           33                 59
D67V4, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           12                 74
  CLUS_2           37                 71
  CLUS_3           28                 82
  CLUS_4            4                 96
D67V5, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           18                 67
  CLUS_2           13                 62
  CLUS_3           19                 56
D67V6, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1            2                 21
  CLUS_2           25                 64
  CLUS_3           17                 48
  CLUS_4            6                 52
D67V7, multiclass
D67V8, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           18                140
  CLUS_2           32                 73
  CLUS_3           30                 98
D67V9, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           19                152
  CLUS_2           55                143
  CLUS_3           20                 78
D67V10, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           17                147
  CLUS_2           64                180
  CLUS_3           13                 46
D67V11, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           22                135
  CLUS_2           46                128
  CLUS_3           13                 60
D67V12, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           19                134
  CLUS_2            9                 37
  CLUS_3           53                152

Clustering(68) Variable = 16p loss
D68V1, multiclass
[1] "Remove cluster labels:" "16P LOSS CNV"          
clus
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1678         TCGA-64-1680 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-67-3774 
"16P LOSS WILD-TYPE" 
D68V2, multiclass
[1] "Remove cluster labels:" "16P LOSS CNV"          
clus
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1678         TCGA-64-1680 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-67-3774 
"16P LOSS WILD-TYPE" 
D68V3, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1           21                166
  CLUS_2            5                209
  CLUS_3           13                 79
D68V4, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            5                 81
  CLUS_2           16                 92
  CLUS_3            9                101
  CLUS_4            3                 97
D68V5, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            8                 77
  CLUS_2            2                 73
  CLUS_3           10                 65
D68V6, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            9                 80
  CLUS_3            8                 57
  CLUS_4            2                 56
D68V7, multiclass
D68V8, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            8                150
  CLUS_2            8                 97
  CLUS_3           15                113
D68V9, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            9                162
  CLUS_2           22                176
  CLUS_3            6                 92
D68V10, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            7                157
  CLUS_2           24                220
  CLUS_3            6                 53
D68V11, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            8                149
  CLUS_2           19                155
  CLUS_3            6                 67
D68V12, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            8                145
  CLUS_2            4                 42
  CLUS_3           21                184

Clustering(69) Variable = 16q loss
D69V1, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            3                  2
  CLUS_2            0                  9
  CLUS_3            2                 10
  CLUS_4            0                  6
D69V2, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            1                  6
  CLUS_2            2                 11
  CLUS_3            2                 10
D69V3, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           36                151
  CLUS_2            5                209
  CLUS_3           16                 76
D69V4, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            8                 78
  CLUS_2           21                 87
  CLUS_3           14                 96
  CLUS_4            4                 96
D69V5, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           10                 75
  CLUS_2            6                 69
  CLUS_3           19                 56
D69V6, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            5                 18
  CLUS_2           11                 78
  CLUS_3           16                 49
  CLUS_4            3                 55
D69V7, multiclass
D69V8, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           15                143
  CLUS_2           17                 88
  CLUS_3           20                108
D69V9, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           16                155
  CLUS_2           34                164
  CLUS_3            7                 91
D69V10, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           15                149
  CLUS_2           35                209
  CLUS_3            7                 52
D69V11, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           13                144
  CLUS_2           30                144
  CLUS_3            4                 69
D69V12, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           13                140
  CLUS_2            5                 41
  CLUS_3           29                176

Clustering(70) Variable = 17p loss
D70V1, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            3                  2
  CLUS_2            2                  7
  CLUS_3            3                  9
  CLUS_4            3                  3
D70V2, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            3                  4
  CLUS_2            3                 10
  CLUS_3            5                  7
D70V3, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           69                118
  CLUS_2           26                188
  CLUS_3           23                 69
D70V4, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           18                 68
  CLUS_2           28                 80
  CLUS_3           34                 76
  CLUS_4            9                 91
D70V5, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           29                 56
  CLUS_2           13                 62
  CLUS_3           19                 56
D70V6, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1            5                 18
  CLUS_2           30                 59
  CLUS_3           15                 50
  CLUS_4           11                 47
D70V7, multiclass
D70V8, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           36                122
  CLUS_2           29                 76
  CLUS_3           28                100
D70V9, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           37                134
  CLUS_2           50                148
  CLUS_3           21                 77
D70V10, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           33                131
  CLUS_2           60                184
  CLUS_3           15                 44
D70V11, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           31                126
  CLUS_2           43                131
  CLUS_3           16                 57
D70V12, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           31                122
  CLUS_2           14                 32
  CLUS_3           45                160

Clustering(71) Variable = 17q loss
D71V1, multiclass
[1] "Remove cluster labels:" "17Q LOSS CNV"          
clus
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-67-3774 
"17Q LOSS WILD-TYPE" 
D71V2, multiclass
[1] "Remove cluster labels:" "17Q LOSS CNV"          
clus
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 1                 31 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-2666         TCGA-44-2668         TCGA-44-3398 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-44-3918         TCGA-44-3919         TCGA-44-4112 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-55-1592         TCGA-55-1594         TCGA-55-1595 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-55-1596         TCGA-64-1676         TCGA-64-1677 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-64-1678         TCGA-64-1680         TCGA-67-3770 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3773 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-67-3774 
"17Q LOSS WILD-TYPE" 
D71V3, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1           11                176
  CLUS_2            4                210
  CLUS_3            4                 88
D71V4, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            6                 80
  CLUS_2            3                105
  CLUS_3            5                105
  CLUS_4            0                100
D71V5, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            8                 77
  CLUS_2            1                 74
  CLUS_3            2                 73
D71V6, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            1                 22
  CLUS_2            6                 83
  CLUS_3            2                 63
  CLUS_4            2                 56
D71V7, multiclass
D71V8, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            6                152
  CLUS_2            6                 99
  CLUS_3            1                127
D71V9, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            4                167
  CLUS_2            7                191
  CLUS_3            4                 94
D71V10, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            1                163
  CLUS_2            9                235
  CLUS_3            5                 54
D71V11, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            4                153
  CLUS_2            7                167
  CLUS_3            3                 70
D71V12, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            3                150
  CLUS_2            3                 43
  CLUS_3            8                197

Clustering(72) Variable = 18p loss
D72V1, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            1                  8
  CLUS_3            1                 11
  CLUS_4            2                  4
D72V2, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            1                 12
  CLUS_3            1                 11
D72V3, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           53                134
  CLUS_2           13                201
  CLUS_3           14                 78
D72V4, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           16                 70
  CLUS_2           23                 85
  CLUS_3           21                 89
  CLUS_4            7                 93
D72V5, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           15                 70
  CLUS_2           11                 64
  CLUS_3           13                 62
D72V6, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1            5                 18
  CLUS_2           18                 71
  CLUS_3           11                 54
  CLUS_4            5                 53
D72V7, multiclass
D72V8, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           23                135
  CLUS_2           21                 84
  CLUS_3           17                111
D72V9, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           25                146
  CLUS_2           35                163
  CLUS_3           13                 85
D72V10, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           26                138
  CLUS_2           37                207
  CLUS_3           10                 49
D72V11, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           16                141
  CLUS_2           36                138
  CLUS_3           14                 59
D72V12, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           23                130
  CLUS_2           11                 35
  CLUS_3           32                173

Clustering(73) Variable = 18q loss
D73V1, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            1                  8
  CLUS_3            1                 11
  CLUS_4            2                  4
D73V2, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            1                 12
  CLUS_3            1                 11
D73V3, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           76                111
  CLUS_2           22                192
  CLUS_3           14                 78
D73V4, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           24                 62
  CLUS_2           29                 79
  CLUS_3           34                 76
  CLUS_4           10                 90
D73V5, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           24                 61
  CLUS_2           14                 61
  CLUS_3           19                 56
D73V6, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1            8                 15
  CLUS_2           23                 66
  CLUS_3           18                 47
  CLUS_4            8                 50
D73V7, multiclass
D73V8, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           32                126
  CLUS_2           34                 71
  CLUS_3           23                105
D73V9, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           31                140
  CLUS_2           53                145
  CLUS_3           21                 77
D73V10, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           36                128
  CLUS_2           55                189
  CLUS_3           14                 45
D73V11, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           27                130
  CLUS_2           50                124
  CLUS_3           19                 54
D73V12, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           34                119
  CLUS_2           14                 32
  CLUS_3           48                157

Clustering(74) Variable = 19p loss
D74V1, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            2                  7
  CLUS_3            3                  9
  CLUS_4            3                  3
D74V2, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            3                  4
  CLUS_2            3                 10
  CLUS_3            3                  9
D74V3, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           51                136
  CLUS_2           33                181
  CLUS_3           35                 57
D74V4, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           21                 65
  CLUS_2           39                 69
  CLUS_3           19                 91
  CLUS_4            6                 94
D74V5, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           22                 63
  CLUS_2           22                 53
  CLUS_3           19                 56
D74V6, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            4                 19
  CLUS_2           24                 65
  CLUS_3           17                 48
  CLUS_4           18                 40
D74V7, multiclass
D74V8, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           35                123
  CLUS_2           23                 82
  CLUS_3           41                 87
D74V9, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           34                137
  CLUS_2           59                139
  CLUS_3           14                 84
D74V10, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           35                129
  CLUS_2           66                178
  CLUS_3            6                 53
D74V11, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           29                128
  CLUS_2           47                127
  CLUS_3            9                 64
D74V12, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           28                125
  CLUS_2            5                 41
  CLUS_3           52                153

Clustering(75) Variable = 19q loss
D75V1, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            0                  5
  CLUS_2            2                  7
  CLUS_3            2                 10
  CLUS_4            2                  4
D75V2, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            2                 11
  CLUS_3            2                 10
D75V3, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           38                149
  CLUS_2           17                197
  CLUS_3           17                 75
D75V4, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           10                 76
  CLUS_2           21                 87
  CLUS_3           14                 96
  CLUS_4            6                 94
D75V5, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           17                 68
  CLUS_2           12                 63
  CLUS_3           11                 64
D75V6, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            2                 21
  CLUS_2           19                 70
  CLUS_3            8                 57
  CLUS_4           11                 47
D75V7, multiclass
D75V8, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           19                139
  CLUS_2           16                 89
  CLUS_3           23                105
D75V9, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           18                153
  CLUS_2           38                160
  CLUS_3            8                 90
D75V10, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           18                146
  CLUS_2           42                202
  CLUS_3            4                 55
D75V11, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           15                142
  CLUS_2           31                143
  CLUS_3            4                 69
D75V12, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           12                141
  CLUS_2            5                 41
  CLUS_3           33                172

Clustering(76) Variable = 20p loss
D76V1, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            1                  4
  CLUS_2            0                  9
  CLUS_3            1                 11
  CLUS_4            2                  4
D76V2, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            2                  5
  CLUS_2            1                 12
  CLUS_3            1                 11
D76V3, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           37                150
  CLUS_2           13                201
  CLUS_3           16                 76
D76V4, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            9                 77
  CLUS_2           13                 95
  CLUS_3           24                 86
  CLUS_4            7                 93
D76V5, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           20                 65
  CLUS_2            4                 71
  CLUS_3           12                 63
D76V6, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            4                 19
  CLUS_2           21                 68
  CLUS_3            8                 57
  CLUS_4            3                 55
D76V7, multiclass
D76V8, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           17                141
  CLUS_2           19                 86
  CLUS_3           17                111
D76V9, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           20                151
  CLUS_2           28                170
  CLUS_3           12                 86
D76V10, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           14                150
  CLUS_2           35                209
  CLUS_3           11                 48
D76V11, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           20                137
  CLUS_2           25                149
  CLUS_3            8                 65
D76V12, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           20                133
  CLUS_2            7                 39
  CLUS_3           26                179

Clustering(77) Variable = 20q loss
D77V1, multiclass
[1] "Remove cluster labels:" "20Q LOSS CNV"          
clus
      20Q LOSS CNV 20Q LOSS WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1680         TCGA-67-3770 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3774 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D77V2, multiclass
[1] "Remove cluster labels:" "20Q LOSS CNV"          
clus
      20Q LOSS CNV 20Q LOSS WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1592         TCGA-55-1594 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-55-1595         TCGA-55-1596         TCGA-64-1676 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-64-1677         TCGA-64-1680         TCGA-67-3770 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-67-3771         TCGA-67-3772         TCGA-67-3774 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D77V3, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            8                179
  CLUS_2            8                206
  CLUS_3            9                 83
D77V4, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            7                 79
  CLUS_2            6                102
  CLUS_3            6                104
  CLUS_4            1                 99
D77V5, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            7                 78
  CLUS_2            2                 73
  CLUS_3            4                 71
D77V6, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            3                 20
  CLUS_2            3                 86
  CLUS_3            4                 61
  CLUS_4            3                 55
D77V7, multiclass
D77V8, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1           11                147
  CLUS_2            3                102
  CLUS_3            6                122
D77V9, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1           10                161
  CLUS_2           11                187
  CLUS_3            3                 95
D77V10, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            6                158
  CLUS_2           14                230
  CLUS_3            4                 55
D77V11, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            9                148
  CLUS_2            9                165
  CLUS_3            2                 71
D77V12, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            6                147
  CLUS_2            3                 43
  CLUS_3           11                194

Clustering(78) Variable = 21q loss
D78V1, multiclass
[1] "Remove cluster labels:" "21Q LOSS CNV"          
clus
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1595         TCGA-55-1596 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-64-1676         TCGA-64-1677         TCGA-64-1678 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-64-1680         TCGA-67-3770         TCGA-67-3771 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
D78V2, multiclass
[1] "Remove cluster labels:" "21Q LOSS CNV"          
clus
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 2                 30 
        TCGA-05-4244         TCGA-05-4249         TCGA-05-4250 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-35-3615         TCGA-35-4122         TCGA-35-4123 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2655         TCGA-44-2656         TCGA-44-2657 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2659         TCGA-44-2661         TCGA-44-2662 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-2665         TCGA-44-2666         TCGA-44-2668 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-3398         TCGA-44-3918         TCGA-44-3919 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-44-4112         TCGA-55-1595         TCGA-55-1596 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-64-1676         TCGA-64-1677         TCGA-64-1678 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-64-1680         TCGA-67-3770         TCGA-67-3771 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-67-3772         TCGA-67-3773         TCGA-67-3774 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
D78V3, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           26                161
  CLUS_2           11                203
  CLUS_3           31                 61
D78V4, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            8                 78
  CLUS_2           32                 76
  CLUS_3           10                100
  CLUS_4            6                 94
D78V5, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            8                 77
  CLUS_2           10                 65
  CLUS_3           16                 59
D78V6, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            2                 21
  CLUS_2            6                 83
  CLUS_3           15                 50
  CLUS_4           11                 47
D78V7, multiclass
D78V8, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           13                145
  CLUS_2            7                 98
  CLUS_3           37                 91
D78V9, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           12                159
  CLUS_2           44                154
  CLUS_3            8                 90
D78V10, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           11                153
  CLUS_2           52                192
  CLUS_3            1                 58
D78V11, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           15                142
  CLUS_2           35                139
  CLUS_3            6                 67
D78V12, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           10                143
  CLUS_2            2                 44
  CLUS_3           44                161

Clustering(79) Variable = 22q loss
D79V1, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            2                  3
  CLUS_2            1                  8
  CLUS_3            1                 11
  CLUS_4            0                  6
D79V2, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            0                  7
  CLUS_2            1                 12
  CLUS_3            3                  9
D79V3, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           51                136
  CLUS_2           14                200
  CLUS_3           32                 60
D79V4, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           11                 75
  CLUS_2           34                 74
  CLUS_3           20                 90
  CLUS_4            9                 91
D79V5, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           20                 65
  CLUS_2           10                 65
  CLUS_3           26                 49
D79V6, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            4                 19
  CLUS_2           19                 70
  CLUS_3           25                 40
  CLUS_4            8                 50
D79V7, multiclass
D79V8, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           22                136
  CLUS_2           20                 85
  CLUS_3           37                 91
D79V9, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           21                150
  CLUS_2           54                144
  CLUS_3           13                 85
D79V10, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           21                143
  CLUS_2           61                183
  CLUS_3            6                 53
D79V11, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           21                136
  CLUS_2           44                130
  CLUS_3            9                 64
D79V12, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           17                136
  CLUS_2            4                 42
  CLUS_3           53                152

Clustering(80) Variable = Xq loss
D80V1, multiclass
[1] "Remove cluster labels:" "XQ LOSS CNV"           
clus
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                2                30 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1594 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-55-1596        TCGA-64-1676        TCGA-64-1677        TCGA-64-1678 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-64-1680        TCGA-67-3770        TCGA-67-3771        TCGA-67-3772 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-67-3773        TCGA-67-3774 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D80V2, multiclass
[1] "Remove cluster labels:" "XQ LOSS CNV"           
clus
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                2                30 
       TCGA-05-4244        TCGA-05-4249        TCGA-05-4250        TCGA-35-3615 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-35-4122        TCGA-35-4123        TCGA-44-2655        TCGA-44-2656 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-2657        TCGA-44-2659        TCGA-44-2661        TCGA-44-2662 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-2665        TCGA-44-2666        TCGA-44-2668        TCGA-44-3398 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-44-3918        TCGA-44-3919        TCGA-44-4112        TCGA-55-1594 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-55-1596        TCGA-64-1676        TCGA-64-1677        TCGA-64-1678 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-64-1680        TCGA-67-3770        TCGA-67-3771        TCGA-67-3772 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-67-3773        TCGA-67-3774 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D80V3, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           5               182
  CLUS_2           3               211
  CLUS_3           3                89
D80V4, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3                83
  CLUS_2           3               105
  CLUS_3           2               108
  CLUS_4           0               100
D80V5, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1                84
  CLUS_2           2                73
  CLUS_3           2                73
D80V6, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                23
  CLUS_2           1                88
  CLUS_3           3                62
  CLUS_4           1                57
D80V7, multiclass
D80V8, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3               155
  CLUS_2           1               104
  CLUS_3           5               123
D80V9, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3               168
  CLUS_2           6               192
  CLUS_3           2                96
D80V10, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3               161
  CLUS_2           8               236
  CLUS_3           0                59
D80V11, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3               154
  CLUS_2           5               169
  CLUS_3           0                73
D80V12, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1               152
  CLUS_2           1                45
  CLUS_3           6               199
                           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")
