
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/4431777/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/LUAD-TP/4469912/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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 5:'RPPA_CNMF':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'RPPA_CHIERARCHICAL':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'MRNASEQ_CNMF':	nDistinctValues=3,	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=3, binary=FALSE, numeric=FALSE
RPPA_CNMF, nv=3, binary=FALSE, numeric=FALSE
RPPA_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CNMF, nv=3, binary=FALSE, numeric=FALSE
MRNASEQ_CHIERARCHICAL, nv=3, binary=FALSE, numeric=FALSE
MIRSEQ_CNMF, nv=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          16               125
  CLUS_2          24               116
  CLUS_3           9               141
D1V5, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          15                79
  CLUS_2           5                63
  CLUS_3           6                67
D1V6, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          18                88
  CLUS_2           6                64
  CLUS_3           2                57
D1V7, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          15               140
  CLUS_2          26               135
  CLUS_3          17               133
D1V8, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          19                99
  CLUS_2          22               186
  CLUS_3          17               123
D1V9, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          18               161
  CLUS_2          29               202
  CLUS_3          10                68
D1V10, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           7                44
  CLUS_2          29               220
  CLUS_3          21               167
D1V11, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1          18               137
  CLUS_2          24               168
  CLUS_3           8                70
D1V12, multiclass
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  CLUS_1           5                44
  CLUS_2          20               168
  CLUS_3          25               163

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          73                68
  CLUS_2          63                77
  CLUS_3          31               119
D2V5, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          31                63
  CLUS_2          34                34
  CLUS_3          19                54
D2V6, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          37                69
  CLUS_2          31                39
  CLUS_3          16                43
D2V7, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          60                95
  CLUS_2          55               106
  CLUS_3          62                88
D2V8, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          41                77
  CLUS_2          82               126
  CLUS_3          54                86
D2V9, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          71               108
  CLUS_2          89               142
  CLUS_3          28                50
D2V10, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          18                33
  CLUS_2          95               154
  CLUS_3          75               113
D2V11, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          68                87
  CLUS_2          76               116
  CLUS_3          23                55
D2V12, multiclass
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  CLUS_1          16                33
  CLUS_2          70               118
  CLUS_3          81               107

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          28               113
  CLUS_2          10               130
  CLUS_3           2               148
D3V5, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           6                88
  CLUS_2           9                59
  CLUS_3          15                58
D3V6, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           8                98
  CLUS_2           8                62
  CLUS_3          14                45
D3V7, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           8               147
  CLUS_2          15               146
  CLUS_3          26               124
D3V8, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           9               109
  CLUS_2          13               195
  CLUS_3          27               113
D3V9, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1          12               167
  CLUS_2          34               197
  CLUS_3           4                74
D3V10, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           3                48
  CLUS_2          36               213
  CLUS_3          11               177
D3V11, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           9               146
  CLUS_2          26               166
  CLUS_3           5                73
D3V12, multiclass
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  CLUS_1           4                45
  CLUS_2          27               161
  CLUS_3           9               179

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          26               115
  CLUS_2          11               129
  CLUS_3           1               149
D4V5, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           5                89
  CLUS_2           9                59
  CLUS_3          10                63
D4V6, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           7                99
  CLUS_2           8                62
  CLUS_3           9                50
D4V7, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           9               146
  CLUS_2           9               152
  CLUS_3          27               123
D4V8, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           7               111
  CLUS_2          15               193
  CLUS_3          23               117
D4V9, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1          11               168
  CLUS_2          32               199
  CLUS_3           2                76
D4V10, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           3                48
  CLUS_2          33               216
  CLUS_3           9               179
D4V11, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           9               146
  CLUS_2          28               164
  CLUS_3           2                76
D4V12, multiclass
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  CLUS_1           2                47
  CLUS_2          27               161
  CLUS_3          10               178

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           4               137
  CLUS_2           8               132
  CLUS_3           1               149
D5V5, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           3                91
  CLUS_2           1                67
  CLUS_3           4                69
D5V6, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           5               101
  CLUS_2           1                69
  CLUS_3           2                57
D5V7, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           0               155
  CLUS_2           9               152
  CLUS_3           4               146
D5V8, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           8               110
  CLUS_2           1               207
  CLUS_3           4               136
D5V9, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           4               175
  CLUS_2           8               223
  CLUS_3           1                77
D5V10, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           1                50
  CLUS_2           8               241
  CLUS_3           4               184
D5V11, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           5               150
  CLUS_2           6               186
  CLUS_3           2                76
D5V12, multiclass
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  CLUS_1           1                48
  CLUS_2           8               180
  CLUS_3           4               184

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          13               128
  CLUS_2          11               129
  CLUS_3           4               146
D6V5, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           5                89
  CLUS_2           2                66
  CLUS_3           9                64
D6V6, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           7                99
  CLUS_2           3                67
  CLUS_3           6                53
D6V7, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           3               152
  CLUS_2          12               149
  CLUS_3          13               137
D6V8, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1          10               108
  CLUS_2           8               200
  CLUS_3          10               130
D6V9, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           7               172
  CLUS_2          21               210
  CLUS_3           2                76
D6V10, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           1                50
  CLUS_2          21               228
  CLUS_3           8               180
D6V11, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           7               148
  CLUS_2          19               173
  CLUS_3           2                76
D6V12, multiclass
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  CLUS_1           3                46
  CLUS_2          17               171
  CLUS_3           8               180

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          15               126
  CLUS_2           9               131
  CLUS_3           3               147
D7V5, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           6                88
  CLUS_2           3                65
  CLUS_3           8                65
D7V6, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           8                98
  CLUS_2           1                69
  CLUS_3           8                51
D7V7, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           7               148
  CLUS_2          12               149
  CLUS_3          10               140
D7V8, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1          11               107
  CLUS_2           8               200
  CLUS_3          10               130
D7V9, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           8               171
  CLUS_2          16               215
  CLUS_3           6                72
D7V10, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           3                48
  CLUS_2          19               230
  CLUS_3           8               180
D7V11, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           8               147
  CLUS_2          13               179
  CLUS_3           5                73
D7V12, multiclass
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  CLUS_1           2                47
  CLUS_2          16               172
  CLUS_3           8               180

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           3               138
  CLUS_2           3               137
  CLUS_3           2               148
D8V5, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           0                94
  CLUS_2           2                66
  CLUS_3           4                69
D8V6, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           1               105
  CLUS_2           1                69
  CLUS_3           4                55
D8V7, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           2               153
  CLUS_2           6               155
  CLUS_3           1               149
D8V8, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           5               113
  CLUS_2           2               206
  CLUS_3           2               138
D8V9, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           1               178
  CLUS_2           4               227
  CLUS_3           5                73
D8V10, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           2                49
  CLUS_2           7               242
  CLUS_3           1               187
D8V11, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           1               154
  CLUS_2           5               187
  CLUS_3           2                76
D8V12, multiclass
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  CLUS_1           2                47
  CLUS_2           6               182
  CLUS_3           0               188

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          57                84
  CLUS_2          57                83
  CLUS_3          47               103
D9V5, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          38                56
  CLUS_2          27                41
  CLUS_3          26                47
D9V6, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          42                64
  CLUS_2          26                44
  CLUS_3          23                36
D9V7, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          55               100
  CLUS_2          67                94
  CLUS_3          55                95
D9V8, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          54                64
  CLUS_2          68               140
  CLUS_3          55                85
D9V9, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          59               120
  CLUS_2          95               136
  CLUS_3          28                50
D9V10, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          20                31
  CLUS_2         101               148
  CLUS_3          61               127
D9V11, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          53               102
  CLUS_2          76               116
  CLUS_3          29                49
D9V12, multiclass
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  CLUS_1          18                31
  CLUS_2          76               112
  CLUS_3          64               124

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               121
  CLUS_2          14               126
  CLUS_3          17               133
D10V5, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          12                82
  CLUS_2          10                58
  CLUS_3           6                67
D10V6, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          15                91
  CLUS_2           9                61
  CLUS_3           4                55
D10V7, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          28               127
  CLUS_2          15               146
  CLUS_3          12               138
D10V8, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          10               108
  CLUS_2          36               172
  CLUS_3           9               131
D10V9, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          26               153
  CLUS_2          23               208
  CLUS_3          11                67
D10V10, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           9                42
  CLUS_2          22               227
  CLUS_3          29               159
D10V11, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1          23               132
  CLUS_2          14               178
  CLUS_3          12                66
D10V12, multiclass
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  CLUS_1           5                44
  CLUS_2          17               171
  CLUS_3          27               161

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          35               106
  CLUS_2          19               121
  CLUS_3           7               143
D11V5, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           6                88
  CLUS_2          17                51
  CLUS_3          11                62
D11V6, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          11                95
  CLUS_2          13                57
  CLUS_3          10                49
D11V7, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          25               130
  CLUS_2          16               145
  CLUS_3          29               121
D11V8, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          12               106
  CLUS_2          34               174
  CLUS_3          24               116
D11V9, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          22               157
  CLUS_2          40               191
  CLUS_3           8                70
D11V10, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           6                45
  CLUS_2          41               208
  CLUS_3          23               165
D11V11, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1          19               136
  CLUS_2          34               158
  CLUS_3           8                70
D11V12, multiclass
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  CLUS_1           6                43
  CLUS_2          32               156
  CLUS_3          23               165

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          11               130
  CLUS_2           6               134
  CLUS_3           1               149
D12V5, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           2                92
  CLUS_2           2                66
  CLUS_3           6                67
D12V6, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           5               101
  CLUS_2           0                70
  CLUS_3           5                54
D12V7, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           6               149
  CLUS_2           4               157
  CLUS_3           9               141
D12V8, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           5               113
  CLUS_2           7               201
  CLUS_3           7               133
D12V9, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           2               177
  CLUS_2          15               216
  CLUS_3           2                76
D12V10, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           2                49
  CLUS_2          15               234
  CLUS_3           2               186
D12V11, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           4               151
  CLUS_2           9               183
  CLUS_3           5                73
D12V12, multiclass
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  CLUS_1           2                47
  CLUS_2          12               176
  CLUS_3           4               184

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          51                90
  CLUS_2          56                84
  CLUS_3          36               114
D13V5, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          44                50
  CLUS_2          13                55
  CLUS_3          29                44
D13V6, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          47                59
  CLUS_2          15                55
  CLUS_3          24                35
D13V7, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          40               115
  CLUS_2          78                83
  CLUS_3          36               114
D13V8, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          66                52
  CLUS_2          47               161
  CLUS_3          41                99
D13V9, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          38               141
  CLUS_2          82               149
  CLUS_3          38                40
D13V10, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          26                25
  CLUS_2          85               164
  CLUS_3          47               141
D13V11, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          37               118
  CLUS_2          72               120
  CLUS_3          33                45
D13V12, multiclass
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  CLUS_1          23                26
  CLUS_2          73               115
  CLUS_3          46               142

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          31               110
  CLUS_2          42                98
  CLUS_3          24               126
D14V5, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          32                62
  CLUS_2          11                57
  CLUS_3          17                56
D14V6, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          33                73
  CLUS_2          13                57
  CLUS_3          14                45
D14V7, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          29               126
  CLUS_2          57               104
  CLUS_3          23               127
D14V8, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          49                69
  CLUS_2          33               175
  CLUS_3          27               113
D14V9, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          30               149
  CLUS_2          56               175
  CLUS_3          24                54
D14V10, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          16                35
  CLUS_2          60               189
  CLUS_3          34               154
D14V11, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          25               130
  CLUS_2          50               142
  CLUS_3          22                56
D14V12, multiclass
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  CLUS_1          14                35
  CLUS_2          51               137
  CLUS_3          32               156

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          27               114
  CLUS_2          18               122
  CLUS_3           8               142
D15V5, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          11                83
  CLUS_2           9                59
  CLUS_3          12                61
D15V6, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          11                95
  CLUS_2           8                62
  CLUS_3          13                46
D15V7, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          14               141
  CLUS_2          14               147
  CLUS_3          29               121
D15V8, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          10               108
  CLUS_2          21               187
  CLUS_3          26               114
D15V9, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          17               162
  CLUS_2          33               198
  CLUS_3           9                69
D15V10, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           7                44
  CLUS_2          37               212
  CLUS_3          15               173
D15V11, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1          15               140
  CLUS_2          28               164
  CLUS_3          10                68
D15V12, multiclass
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  CLUS_1           7                42
  CLUS_2          23               165
  CLUS_3          23               165

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          58                83
  CLUS_2          54                86
  CLUS_3          19               131
D16V5, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          31                63
  CLUS_2          17                51
  CLUS_3          28                45
D16V6, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          36                70
  CLUS_2          14                56
  CLUS_3          26                33
D16V7, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          30               125
  CLUS_2          52               109
  CLUS_3          58                92
D16V8, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          38                80
  CLUS_2          42               166
  CLUS_3          60                80
D16V9, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          28               151
  CLUS_2          95               136
  CLUS_3          24                54
D16V10, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          11                40
  CLUS_2         103               146
  CLUS_3          33               155
D16V11, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          31               124
  CLUS_2          74               118
  CLUS_3          24                54
D16V12, multiclass
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  CLUS_1          14                35
  CLUS_2          75               113
  CLUS_3          40               148

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           6               135
  CLUS_2           8               132
  CLUS_3           2               148
D17V5, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           2                92
  CLUS_2           2                66
  CLUS_3           1                72
D17V6, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3               103
  CLUS_2           1                69
  CLUS_3           1                58
D17V7, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           4               151
  CLUS_2           6               155
  CLUS_3           5               145
D17V8, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           6               112
  CLUS_2           4               204
  CLUS_3           5               135
D17V9, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           4               175
  CLUS_2          11               220
  CLUS_3           1                77
D17V10, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1                50
  CLUS_2          11               238
  CLUS_3           4               184
D17V11, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           3               152
  CLUS_2          12               180
  CLUS_3           1                77
D17V12, multiclass
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  CLUS_1           1                48
  CLUS_2          12               176
  CLUS_3           3               185

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           3               138
  CLUS_2           3               137
  CLUS_3           2               148
D18V5, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           0                94
  CLUS_2           2                66
  CLUS_3           2                71
D18V6, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1               105
  CLUS_2           1                69
  CLUS_3           2                57
D18V7, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           3               152
  CLUS_2           2               159
  CLUS_3           3               147
D18V8, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2               116
  CLUS_2           3               205
  CLUS_3           3               137
D18V9, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1               178
  CLUS_2           5               226
  CLUS_3           2                76
D18V10, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                49
  CLUS_2           5               244
  CLUS_3           1               187
D18V11, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           1               154
  CLUS_2           5               187
  CLUS_3           2                76
D18V12, multiclass
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  CLUS_1           2                47
  CLUS_2           6               182
  CLUS_3           0               188

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           20                121
  CLUS_2           21                119
  CLUS_3            4                146
D19V5, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            8                 86
  CLUS_2           11                 57
  CLUS_3           10                 63
D19V6, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            9                 97
  CLUS_2           10                 60
  CLUS_3           10                 49
D19V7, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            8                147
  CLUS_2           14                147
  CLUS_3           27                123
D19V8, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           11                107
  CLUS_2           14                194
  CLUS_3           24                116
D19V9, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           15                164
  CLUS_2           31                200
  CLUS_3            3                 75
D19V10, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            3                 48
  CLUS_2           31                218
  CLUS_3           15                173
D19V11, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1           17                138
  CLUS_2           27                165
  CLUS_3            2                 76
D19V12, multiclass
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  CLUS_1            3                 46
  CLUS_2           25                163
  CLUS_3           18                170

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           14                127
  CLUS_2            9                131
  CLUS_3            1                149
D20V5, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            6                 88
  CLUS_2            7                 61
  CLUS_3            2                 71
D20V6, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            3                103
  CLUS_2            8                 62
  CLUS_3            4                 55
D20V7, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            7                148
  CLUS_2            4                157
  CLUS_3           16                134
D20V8, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            3                115
  CLUS_2           11                197
  CLUS_3           13                127
D20V9, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1           12                167
  CLUS_2           15                216
  CLUS_3            1                 77
D20V10, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            2                 49
  CLUS_2           16                233
  CLUS_3           10                178
D20V11, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            9                146
  CLUS_2           14                178
  CLUS_3            2                 76
D20V12, multiclass
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  CLUS_1            2                 47
  CLUS_2           10                178
  CLUS_3           13                175

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           12                129
  CLUS_2           15                125
  CLUS_3            3                147
D21V5, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            8                 86
  CLUS_2            3                 65
  CLUS_3            6                 67
D21V6, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            8                 98
  CLUS_2            4                 66
  CLUS_3            5                 54
D21V7, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            8                147
  CLUS_2           12                149
  CLUS_3           15                135
D21V8, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1           10                108
  CLUS_2           10                198
  CLUS_3           15                125
D21V9, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            7                172
  CLUS_2           21                210
  CLUS_3            8                 70
D21V10, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            6                 45
  CLUS_2           22                227
  CLUS_3            8                180
D21V11, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            6                149
  CLUS_2           17                175
  CLUS_3            7                 71
D21V12, multiclass
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  CLUS_1            6                 43
  CLUS_2           15                173
  CLUS_3            9                179

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           15                126
  CLUS_2           23                117
  CLUS_3            6                144
D22V5, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1           10                 84
  CLUS_2            3                 65
  CLUS_3           15                 58
D22V6, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1           13                 93
  CLUS_2            4                 66
  CLUS_3           11                 48
D22V7, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            7                148
  CLUS_2           20                141
  CLUS_3           23                127
D22V8, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1           18                100
  CLUS_2            9                199
  CLUS_3           23                117
D22V9, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            8                171
  CLUS_2           31                200
  CLUS_3           11                 67
D22V10, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            6                 45
  CLUS_2           34                215
  CLUS_3           10                178
D22V11, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            8                147
  CLUS_2           24                168
  CLUS_3           11                 67
D22V12, multiclass
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  CLUS_1            7                 42
  CLUS_2           24                164
  CLUS_3           12                176

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           22                119
  CLUS_2           18                122
  CLUS_3            8                142
D23V5, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           13                 81
  CLUS_2            4                 64
  CLUS_3           12                 61
D23V6, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           11                 95
  CLUS_2            4                 66
  CLUS_3           14                 45
D23V7, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            7                148
  CLUS_2           19                142
  CLUS_3           30                120
D23V8, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           15                103
  CLUS_2           10                198
  CLUS_3           31                109
D23V9, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1           10                169
  CLUS_2           40                191
  CLUS_3            8                 70
D23V10, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            5                 46
  CLUS_2           40                209
  CLUS_3           13                175
D23V11, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            6                149
  CLUS_2           33                159
  CLUS_3            8                 70
D23V12, multiclass
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  CLUS_1            4                 45
  CLUS_2           32                156
  CLUS_3           11                177

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           18                123
  CLUS_2           13                127
  CLUS_3            6                144
D24V5, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            9                 85
  CLUS_2            3                 65
  CLUS_3           11                 62
D24V6, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            8                 98
  CLUS_2            3                 67
  CLUS_3           12                 47
D24V7, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            6                149
  CLUS_2           14                147
  CLUS_3           25                125
D24V8, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           11                107
  CLUS_2            9                199
  CLUS_3           25                115
D24V9, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1           10                169
  CLUS_2           30                201
  CLUS_3            7                 71
D24V10, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            5                 46
  CLUS_2           31                218
  CLUS_3           11                177
D24V11, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            5                150
  CLUS_2           24                168
  CLUS_3            7                 71
D24V12, multiclass
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  CLUS_1            4                 45
  CLUS_2           23                165
  CLUS_3            9                179

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           11                130
  CLUS_2            1                139
  CLUS_3            0                150
D25V5, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            1                 93
  CLUS_2            4                 64
  CLUS_3            6                 67
D25V6, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            2                104
  CLUS_2            3                 67
  CLUS_3            6                 53
D25V7, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            5                150
  CLUS_2            2                159
  CLUS_3            9                141
D25V8, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            2                116
  CLUS_2            7                201
  CLUS_3            7                133
D25V9, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            5                174
  CLUS_2            9                222
  CLUS_3            1                 77
D25V10, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            0                 51
  CLUS_2           10                239
  CLUS_3            5                183
D25V11, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            5                150
  CLUS_2            5                187
  CLUS_3            2                 76
D25V12, multiclass
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  CLUS_1            0                 49
  CLUS_2            7                181
  CLUS_3            5                183

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           30                111
  CLUS_2           17                123
  CLUS_3            8                142
D26V5, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           12                 82
  CLUS_2            6                 62
  CLUS_3           13                 60
D26V6, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           13                 93
  CLUS_2            7                 63
  CLUS_3           11                 48
D26V7, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           14                141
  CLUS_2           17                144
  CLUS_3           24                126
D26V8, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           12                106
  CLUS_2           18                190
  CLUS_3           25                115
D26V9, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           10                169
  CLUS_2           36                195
  CLUS_3           12                 66
D26V10, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            8                 43
  CLUS_2           40                209
  CLUS_3           10                178
D26V11, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1           11                144
  CLUS_2           35                157
  CLUS_3            9                 69
D26V12, multiclass
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  CLUS_1            6                 43
  CLUS_2           35                153
  CLUS_3           14                174

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            4                137
  CLUS_2            5                135
  CLUS_3            1                149
D27V5, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            4                 90
  CLUS_2            2                 66
  CLUS_3            2                 71
D27V6, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            4                102
  CLUS_2            2                 68
  CLUS_3            2                 57
D27V7, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            6                149
  CLUS_2            1                160
  CLUS_3            7                143
D27V8, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                117
  CLUS_2            7                201
  CLUS_3            6                134
D27V9, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            6                173
  CLUS_2            7                224
  CLUS_3            0                 78
D27V10, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            1                 50
  CLUS_2            5                244
  CLUS_3            7                181
D27V11, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            5                150
  CLUS_2            3                189
  CLUS_3            2                 76
D27V12, multiclass
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  CLUS_1            0                 49
  CLUS_2            3                185
  CLUS_3            7                181

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           23                118
  CLUS_2           15                125
  CLUS_3           23                127
D28V5, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           16                 78
  CLUS_2            6                 62
  CLUS_3            9                 64
D28V6, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           17                 89
  CLUS_2            5                 65
  CLUS_3            9                 50
D28V7, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           32                123
  CLUS_2           22                139
  CLUS_3           11                139
D28V8, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           17                101
  CLUS_2           36                172
  CLUS_3           12                128
D28V9, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           28                151
  CLUS_2           25                206
  CLUS_3           17                 61
D28V10, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           13                 38
  CLUS_2           28                221
  CLUS_3           29                159
D28V11, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1           29                126
  CLUS_2           18                174
  CLUS_3           14                 64
D28V12, multiclass
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  CLUS_1            9                 40
  CLUS_2           23                165
  CLUS_3           29                159

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           13                128
  CLUS_2           10                130
  CLUS_3           14                136
D29V5, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           13                 81
  CLUS_2            2                 66
  CLUS_3            7                 66
D29V6, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           14                 92
  CLUS_2            2                 68
  CLUS_3            6                 53
D29V7, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           19                136
  CLUS_2           16                145
  CLUS_3            6                144
D29V8, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           11                107
  CLUS_2           21                187
  CLUS_3            9                131
D29V9, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           15                164
  CLUS_2           14                217
  CLUS_3           13                 65
D29V10, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            8                 43
  CLUS_2           18                231
  CLUS_3           16                172
D29V11, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1           18                137
  CLUS_2           11                181
  CLUS_3            8                 70
D29V12, multiclass
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  CLUS_1            5                 44
  CLUS_2           14                174
  CLUS_3           18                170

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           17                124
  CLUS_2            4                136
  CLUS_3            2                148
D30V5, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            3                 91
  CLUS_2            5                 63
  CLUS_3            2                 71
D30V6, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            5                101
  CLUS_2            4                 66
  CLUS_3            1                 58
D30V7, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            8                147
  CLUS_2            9                152
  CLUS_3           12                138
D30V8, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            6                112
  CLUS_2           10                198
  CLUS_3           13                127
D30V9, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            8                171
  CLUS_2           19                212
  CLUS_3            1                 77
D30V10, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            2                 49
  CLUS_2           18                231
  CLUS_3            8                180
D30V11, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            7                148
  CLUS_2           13                179
  CLUS_3            3                 75
D30V12, multiclass
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  CLUS_1            1                 48
  CLUS_2           15                173
  CLUS_3            7                181

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           33                108
  CLUS_2           30                110
  CLUS_3            6                144
D31V5, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           16                 78
  CLUS_2            9                 59
  CLUS_3           11                 62
D31V6, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           18                 88
  CLUS_2            8                 62
  CLUS_3           10                 49
D31V7, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           19                136
  CLUS_2           33                128
  CLUS_3           24                126
D31V8, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           27                 91
  CLUS_2           26                182
  CLUS_3           23                117
D31V9, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           20                159
  CLUS_2           48                183
  CLUS_3           11                 67
D31V10, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            5                 46
  CLUS_2           51                198
  CLUS_3           23                165
D31V11, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1           20                135
  CLUS_2           36                156
  CLUS_3           13                 65
D31V12, multiclass
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  CLUS_1            6                 43
  CLUS_2           42                146
  CLUS_3           21                167

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           22                119
  CLUS_2           13                127
  CLUS_3            5                145
D32V5, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            4                 90
  CLUS_2           11                 57
  CLUS_3            5                 68
D32V6, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            5                101
  CLUS_2            9                 61
  CLUS_3            6                 53
D32V7, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            9                146
  CLUS_2           14                147
  CLUS_3           21                129
D32V8, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1           11                107
  CLUS_2           12                196
  CLUS_3           21                119
D32V9, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            9                170
  CLUS_2           29                202
  CLUS_3            6                 72
D32V10, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            3                 48
  CLUS_2           33                216
  CLUS_3            8                180
D32V11, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            9                146
  CLUS_2           26                166
  CLUS_3            5                 73
D32V12, multiclass
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  CLUS_1            2                 47
  CLUS_2           30                158
  CLUS_3            8                180

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           16                125
  CLUS_2            4                136
  CLUS_3            3                147
D33V5, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                 92
  CLUS_2            5                 63
  CLUS_3            7                 66
D33V6, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                104
  CLUS_2            6                 64
  CLUS_3            6                 53
D33V7, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            4                151
  CLUS_2            7                154
  CLUS_3           16                134
D33V8, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            6                112
  CLUS_2            4                204
  CLUS_3           17                123
D33V9, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            6                173
  CLUS_2           17                214
  CLUS_3            4                 74
D33V10, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            2                 49
  CLUS_2           21                228
  CLUS_3            4                184
D33V11, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            4                151
  CLUS_2           16                176
  CLUS_3            3                 75
D33V12, multiclass
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  CLUS_1            1                 48
  CLUS_2           17                171
  CLUS_3            5                183

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            3                138
  CLUS_2            0                140
  CLUS_3            1                149
D34V5, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                 92
  CLUS_2            0                 68
  CLUS_3            1                 72
D34V6, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                105
  CLUS_2            1                 69
  CLUS_3            1                 58
D34V7, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                153
  CLUS_2            2                159
  CLUS_3            2                148
D34V8, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                116
  CLUS_2            2                206
  CLUS_3            2                138
D34V9, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                177
  CLUS_2            3                228
  CLUS_3            1                 77
D34V10, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            2                 49
  CLUS_2            3                246
  CLUS_3            1                187
D34V11, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            1                154
  CLUS_2            2                190
  CLUS_3            0                 78
D34V12, multiclass
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  CLUS_1            0                 49
  CLUS_2            2                186
  CLUS_3            1                187

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           15                126
  CLUS_2            4                136
  CLUS_3            3                147
D35V5, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            3                 91
  CLUS_2            2                 66
  CLUS_3            5                 68
D35V6, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            2                104
  CLUS_2            3                 67
  CLUS_3            5                 54
D35V7, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            6                149
  CLUS_2            5                156
  CLUS_3           12                138
D35V8, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            3                115
  CLUS_2            7                201
  CLUS_3           13                127
D35V9, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            6                173
  CLUS_2           15                216
  CLUS_3            3                 75
D35V10, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            1                 50
  CLUS_2           18                231
  CLUS_3            5                183
D35V11, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            5                150
  CLUS_2           14                178
  CLUS_3            3                 75
D35V12, multiclass
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  CLUS_1            1                 48
  CLUS_2           14                174
  CLUS_3            7                181

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           32                109
  CLUS_2           15                125
  CLUS_3            8                142
D36V5, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           13                 81
  CLUS_2            6                 62
  CLUS_3           15                 58
D36V6, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           16                 90
  CLUS_2            9                 61
  CLUS_3            9                 50
D36V7, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           15                140
  CLUS_2           14                147
  CLUS_3           32                118
D36V8, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           10                108
  CLUS_2           17                191
  CLUS_3           34                106
D36V9, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           13                166
  CLUS_2           39                192
  CLUS_3           11                 67
D36V10, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            8                 43
  CLUS_2           42                207
  CLUS_3           13                175
D36V11, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1           11                144
  CLUS_2           33                159
  CLUS_3           12                 66
D36V12, multiclass
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  CLUS_1            9                 40
  CLUS_2           31                157
  CLUS_3           16                172

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           42                 99
  CLUS_2           16                124
  CLUS_3            9                141
D37V5, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           15                 79
  CLUS_2            7                 61
  CLUS_3           22                 51
D37V6, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           21                 85
  CLUS_2            9                 61
  CLUS_3           14                 45
D37V7, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           16                139
  CLUS_2           20                141
  CLUS_3           39                111
D37V8, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           15                103
  CLUS_2           22                186
  CLUS_3           38                102
D37V9, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           16                163
  CLUS_2           50                181
  CLUS_3           12                 66
D37V10, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            7                 44
  CLUS_2           54                195
  CLUS_3           17                171
D37V11, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1           17                138
  CLUS_2           41                151
  CLUS_3           10                 68
D37V12, multiclass
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  CLUS_1            8                 41
  CLUS_2           41                147
  CLUS_3           19                169

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           14                127
  CLUS_2           17                123
  CLUS_3            6                144
D38V5, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           12                 82
  CLUS_2            3                 65
  CLUS_3            7                 66
D38V6, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           14                 92
  CLUS_2            3                 67
  CLUS_3            5                 54
D38V7, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           17                138
  CLUS_2           16                145
  CLUS_3            8                142
D38V8, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           14                104
  CLUS_2           20                188
  CLUS_3            7                133
D38V9, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            8                171
  CLUS_2           28                203
  CLUS_3            6                 72
D38V10, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            7                 44
  CLUS_2           25                224
  CLUS_3           10                178
D38V11, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1           12                143
  CLUS_2           19                173
  CLUS_3            6                 72
D38V12, multiclass
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  CLUS_1            4                 45
  CLUS_2           20                168
  CLUS_3           13                175

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            6                135
  CLUS_2            4                136
  CLUS_3            6                144
D39V5, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            4                 90
  CLUS_2            1                 67
  CLUS_3            5                 68
D39V6, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            5                101
  CLUS_2            2                 68
  CLUS_3            3                 56
D39V7, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            7                148
  CLUS_2            7                154
  CLUS_3            6                144
D39V8, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            6                112
  CLUS_2            9                199
  CLUS_3            5                135
D39V9, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            4                175
  CLUS_2           11                220
  CLUS_3            5                 73
D39V10, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            5                 46
  CLUS_2           11                238
  CLUS_3            4                184
D39V11, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            3                152
  CLUS_2            7                185
  CLUS_3            6                 72
D39V12, multiclass
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  CLUS_1            4                 45
  CLUS_2            8                180
  CLUS_3            4                184

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           5               136
  CLUS_2           5               135
  CLUS_3           3               147
D40V5, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           5                89
  CLUS_2           3                65
  CLUS_3           1                72
D40V6, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           7                99
  CLUS_2           2                68
  CLUS_3           0                59
D40V7, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           3               152
  CLUS_2          10               151
  CLUS_3           4               146
D40V8, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           6               112
  CLUS_2           7               201
  CLUS_3           4               136
D40V9, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           4               175
  CLUS_2           8               223
  CLUS_3           5                73
D40V10, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           2                49
  CLUS_2          11               238
  CLUS_3           4               184
D40V11, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           3               152
  CLUS_2           6               186
  CLUS_3           4                74
D40V12, multiclass
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  CLUS_1           2                47
  CLUS_2           9               179
  CLUS_3           2               186

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          20               121
  CLUS_2           4               136
  CLUS_3           2               148
D41V5, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           6                88
  CLUS_2           5                63
  CLUS_3           7                66
D41V6, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           5               101
  CLUS_2           6                64
  CLUS_3           7                52
D41V7, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           3               152
  CLUS_2           6               155
  CLUS_3          18               132
D41V8, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           5               113
  CLUS_2          10               198
  CLUS_3          12               128
D41V9, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1          11               168
  CLUS_2          13               218
  CLUS_3           4                74
D41V10, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1                50
  CLUS_2          19               230
  CLUS_3           8               180
D41V11, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1          10               145
  CLUS_2          13               179
  CLUS_3           3                75
D41V12, multiclass
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  CLUS_1           1                48
  CLUS_2          17               171
  CLUS_3           8               180

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           7               134
  CLUS_2           1               139
  CLUS_3           1               149
D42V5, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2                92
  CLUS_2           2                66
  CLUS_3           4                69
D42V6, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2               104
  CLUS_2           1                69
  CLUS_3           5                54
D42V7, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           0               155
  CLUS_2           3               158
  CLUS_3           7               143
D42V8, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2               116
  CLUS_2           3               205
  CLUS_3           5               135
D42V9, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           2               177
  CLUS_2           5               226
  CLUS_3           3                75
D42V10, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           1                50
  CLUS_2           8               241
  CLUS_3           1               187
D42V11, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           1               154
  CLUS_2           6               186
  CLUS_3           2                76
D42V12, multiclass
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  CLUS_1           1                48
  CLUS_2           7               181
  CLUS_3           1               187

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               139
  CLUS_2           2               138
  CLUS_3           2               148
D43V5, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1                93
  CLUS_2           1                67
  CLUS_3           1                72
D43V6, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1               105
  CLUS_2           0                70
  CLUS_3           2                57
D43V7, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2               153
  CLUS_2           2               159
  CLUS_3           2               148
D43V8, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2               116
  CLUS_2           2               206
  CLUS_3           2               138
D43V9, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2               177
  CLUS_2           2               229
  CLUS_3           2                76
D43V10, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           1                50
  CLUS_2           3               246
  CLUS_3           2               186
D43V11, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           2               153
  CLUS_2           2               190
  CLUS_3           1                77
D43V12, multiclass
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  CLUS_1           0                49
  CLUS_2           3               185
  CLUS_3           2               186

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               139
  CLUS_2           2               138
  CLUS_3           0               150
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
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               154
  CLUS_2           2               159
  CLUS_3           1               149
D44V8, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           2               116
  CLUS_2           1               207
  CLUS_3           1               139
D44V9, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               178
  CLUS_2           3               228
  CLUS_3           0                78
D44V10, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0                51
  CLUS_2           3               246
  CLUS_3           1               187
D44V11, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           1               154
  CLUS_2           2               190
  CLUS_3           1                77
D44V12, multiclass
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  CLUS_1           0                49
  CLUS_2           3               185
  CLUS_3           1               187

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          51                90
  CLUS_2          24               116
  CLUS_3          10               140
D45V5, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          17                77
  CLUS_2           9                59
  CLUS_3          18                55
D45V6, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          24                82
  CLUS_2           8                62
  CLUS_3          12                47
D45V7, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          21               134
  CLUS_2          26               135
  CLUS_3          43               107
D45V8, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          20                98
  CLUS_2          32               176
  CLUS_3          38               102
D45V9, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          24               155
  CLUS_2          56               175
  CLUS_3          13                65
D45V10, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           9                42
  CLUS_2          58               191
  CLUS_3          26               162
D45V11, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1          25               130
  CLUS_2          49               143
  CLUS_3          10                68
D45V12, multiclass
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  CLUS_1           9                40
  CLUS_2          46               142
  CLUS_3          29               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          34               107
  CLUS_2          16               124
  CLUS_3           2               148
D46V5, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           7                87
  CLUS_2           7                61
  CLUS_3           9                64
D46V6, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          10                96
  CLUS_2           7                63
  CLUS_3           6                53
D46V7, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          17               138
  CLUS_2          11               150
  CLUS_3          25               125
D46V8, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           9               109
  CLUS_2          24               184
  CLUS_3          20               120
D46V9, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          18               161
  CLUS_2          32               199
  CLUS_3           5                73
D46V10, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           4                47
  CLUS_2          33               216
  CLUS_3          18               170
D46V11, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1          21               134
  CLUS_2          27               165
  CLUS_3           3                75
D46V12, multiclass
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  CLUS_1           4                45
  CLUS_2          29               159
  CLUS_3          18               170

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          19               122
  CLUS_2           8               132
  CLUS_3           6               144
D47V5, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           8                86
  CLUS_2           6                62
  CLUS_3          11                62
D47V6, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1          11                95
  CLUS_2           6                64
  CLUS_3           8                51
D47V7, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           5               150
  CLUS_2          10               151
  CLUS_3          23               127
D47V8, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           8               110
  CLUS_2           8               200
  CLUS_3          22               118
D47V9, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           8               171
  CLUS_2          29               202
  CLUS_3           2                76
D47V10, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           1                50
  CLUS_2          29               220
  CLUS_3           9               179
D47V11, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           8               147
  CLUS_2          23               169
  CLUS_3           2                76
D47V12, multiclass
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  CLUS_1           0                49
  CLUS_2          22               166
  CLUS_3          11               177

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          27               114
  CLUS_2           7               133
  CLUS_3           4               146
D48V5, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          10                84
  CLUS_2           8                60
  CLUS_3          10                63
D48V6, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1          13                93
  CLUS_2           6                64
  CLUS_3           9                50
D48V7, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           6               149
  CLUS_2          11               150
  CLUS_3          28               122
D48V8, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           6               112
  CLUS_2          10               198
  CLUS_3          29               111
D48V9, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           8               171
  CLUS_2          33               198
  CLUS_3           5                73
D48V10, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           3                48
  CLUS_2          36               213
  CLUS_3           7               181
D48V11, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           8               147
  CLUS_2          27               165
  CLUS_3           3                75
D48V12, multiclass
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  CLUS_1           2                47
  CLUS_2          25               163
  CLUS_3          11               177

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           5               136
  CLUS_2           4               136
  CLUS_3           0               150
D49V5, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1                93
  CLUS_2           2                66
  CLUS_3           1                72
D49V6, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2               104
  CLUS_2           1                69
  CLUS_3           1                58
D49V7, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0               155
  CLUS_2           4               157
  CLUS_3           7               143
D49V8, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1               117
  CLUS_2           1               207
  CLUS_3           9               131
D49V9, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0               179
  CLUS_2           8               223
  CLUS_3           2                76
D49V10, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           2                49
  CLUS_2           7               242
  CLUS_3           1               187
D49V11, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           0               155
  CLUS_2           7               185
  CLUS_3           1                77
D49V12, multiclass
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  CLUS_1           1                48
  CLUS_2           7               181
  CLUS_3           0               188

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          29               112
  CLUS_2          20               120
  CLUS_3           3               147
D50V5, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          16                78
  CLUS_2           5                63
  CLUS_3          13                60
D50V6, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          15                91
  CLUS_2           7                63
  CLUS_3          12                47
D50V7, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           6               149
  CLUS_2          21               140
  CLUS_3          28               122
D50V8, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          13               105
  CLUS_2          14               194
  CLUS_3          28               112
D50V9, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          12               167
  CLUS_2          38               193
  CLUS_3           8                70
D50V10, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           6                45
  CLUS_2          39               210
  CLUS_3          13               175
D50V11, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1          13               142
  CLUS_2          34               158
  CLUS_3           4                74
D50V12, multiclass
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  CLUS_1           4                45
  CLUS_2          33               155
  CLUS_3          14               174

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          18               123
  CLUS_2          16               124
  CLUS_3           3               147
D51V5, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           7                87
  CLUS_2           3                65
  CLUS_3           9                64
D51V6, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           9                97
  CLUS_2           4                66
  CLUS_3           6                53
D51V7, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           9               146
  CLUS_2          17               144
  CLUS_3          12               138
D51V8, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          13               105
  CLUS_2          14               194
  CLUS_3          11               129
D51V9, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          15               164
  CLUS_2          23               208
  CLUS_3           5                73
D51V10, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           6                45
  CLUS_2          23               226
  CLUS_3          14               174
D51V11, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1          14               141
  CLUS_2          19               173
  CLUS_3           4                74
D51V12, multiclass
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  CLUS_1           5                44
  CLUS_2          14               174
  CLUS_3          18               170

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          44                97
  CLUS_2          43                97
  CLUS_3          14               136
D52V5, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          15                79
  CLUS_2          13                55
  CLUS_3          19                54
D52V6, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          15                91
  CLUS_2          18                52
  CLUS_3          14                45
D52V7, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          29               126
  CLUS_2          37               124
  CLUS_3          35               115
D52V8, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          27                91
  CLUS_2          48               160
  CLUS_3          26               114
D52V9, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          42               137
  CLUS_2          54               177
  CLUS_3          15                63
D52V10, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          16                35
  CLUS_2          54               195
  CLUS_3          41               147
D52V11, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          37               118
  CLUS_2          51               141
  CLUS_3          13                65
D52V12, multiclass
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  CLUS_1          16                33
  CLUS_2          39               149
  CLUS_3          46               142

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           6               135
  CLUS_2           3               137
  CLUS_3           1               149
D53V5, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           2                92
  CLUS_2           2                66
  CLUS_3           2                71
D53V6, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           3               103
  CLUS_2           2                68
  CLUS_3           1                58
D53V7, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           5               150
  CLUS_2           2               159
  CLUS_3           7               143
D53V8, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1               117
  CLUS_2           7               201
  CLUS_3           6               134
D53V9, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           7               172
  CLUS_2           7               224
  CLUS_3           0                78
D53V10, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1                50
  CLUS_2           8               241
  CLUS_3           5               183
D53V11, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           4               151
  CLUS_2           5               187
  CLUS_3           1                77
D53V12, multiclass
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  CLUS_1           1                48
  CLUS_2           5               183
  CLUS_3           4               184

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           6               135
  CLUS_2           3               137
  CLUS_3           3               147
D54V5, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           3                91
  CLUS_2           1                67
  CLUS_3           2                71
D54V6, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           4               102
  CLUS_2           1                69
  CLUS_3           1                58
D54V7, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           7               148
  CLUS_2           3               158
  CLUS_3           7               143
D54V8, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           2               116
  CLUS_2           9               199
  CLUS_3           6               134
D54V9, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           6               173
  CLUS_2           9               222
  CLUS_3           2                76
D54V10, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           3                48
  CLUS_2           9               240
  CLUS_3           5               183
D54V11, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           3               152
  CLUS_2           5               187
  CLUS_3           4                74
D54V12, multiclass
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  CLUS_1           3                46
  CLUS_2           6               182
  CLUS_3           3               185

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          41               100
  CLUS_2          44                96
  CLUS_3          19               131
D55V5, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          28                66
  CLUS_2          12                56
  CLUS_3          22                51
D55V6, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          34                72
  CLUS_2          12                58
  CLUS_3          16                43
D55V7, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          35               120
  CLUS_2          50               111
  CLUS_3          30               120
D55V8, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          44                74
  CLUS_2          47               161
  CLUS_3          24               116
D55V9, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          34               145
  CLUS_2          70               161
  CLUS_3          17                61
D55V10, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1           8                43
  CLUS_2          74               175
  CLUS_3          39               149
D55V11, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          28               127
  CLUS_2          58               134
  CLUS_3          17                61
D55V12, multiclass
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  CLUS_1          12                37
  CLUS_2          61               127
  CLUS_3          30               158

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           5               136
  CLUS_2           9               131
  CLUS_3           5               145
D56V5, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           8                86
  CLUS_2           0                68
  CLUS_3           1                72
D56V6, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           7                99
  CLUS_2           1                69
  CLUS_3           1                58
D56V7, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           7               148
  CLUS_2          11               150
  CLUS_3           2               148
D56V8, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1          11               107
  CLUS_2           8               200
  CLUS_3           1               139
D56V9, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           7               172
  CLUS_2           8               223
  CLUS_3           6                72
D56V10, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           2                49
  CLUS_2          11               238
  CLUS_3           8               180
D56V11, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           6               149
  CLUS_2           7               185
  CLUS_3           6                72
D56V12, multiclass
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  CLUS_1           4                45
  CLUS_2           8               180
  CLUS_3           7               181

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          61                80
  CLUS_2          39               101
  CLUS_3          23               127
D57V5, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          24                70
  CLUS_2          19                49
  CLUS_3          29                44
D57V6, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          26                80
  CLUS_2          21                49
  CLUS_3          25                34
D57V7, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          41               114
  CLUS_2          42               119
  CLUS_3          52                98
D57V8, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          27                91
  CLUS_2          56               152
  CLUS_3          52                88
D57V9, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          49               130
  CLUS_2          67               164
  CLUS_3          23                55
D57V10, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          11                40
  CLUS_2          78               171
  CLUS_3          50               138
D57V11, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          42               113
  CLUS_2          55               137
  CLUS_3          25                53
D57V12, multiclass
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  CLUS_1          12                37
  CLUS_2          60               128
  CLUS_3          50               138

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          56                85
  CLUS_2          28               112
  CLUS_3          17               133
D58V5, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          22                72
  CLUS_2          14                54
  CLUS_3          20                53
D58V6, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          24                82
  CLUS_2          13                57
  CLUS_3          19                40
D58V7, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          29               126
  CLUS_2          37               124
  CLUS_3          47               103
D58V8, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          24                94
  CLUS_2          42               166
  CLUS_3          47                93
D58V9, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          35               144
  CLUS_2          64               167
  CLUS_3          18                60
D58V10, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          10                41
  CLUS_2          69               180
  CLUS_3          38               150
D58V11, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          29               126
  CLUS_2          50               142
  CLUS_3          21                57
D58V12, multiclass
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  CLUS_1          12                37
  CLUS_2          55               133
  CLUS_3          33               155

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           15                126
  CLUS_2           16                124
  CLUS_3            3                147
D59V5, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            8                 86
  CLUS_2            2                 66
  CLUS_3            9                 64
D59V6, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           13                 93
  CLUS_2            3                 67
  CLUS_3            3                 56
D59V7, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            7                148
  CLUS_2           13                148
  CLUS_3           14                136
D59V8, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           10                108
  CLUS_2           10                198
  CLUS_3           14                126
D59V9, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            7                172
  CLUS_2           20                211
  CLUS_3           11                 67
D59V10, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           10                 41
  CLUS_2           20                229
  CLUS_3            8                180
D59V11, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1            4                151
  CLUS_2           18                174
  CLUS_3           12                 66
D59V12, multiclass
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  CLUS_1           11                 38
  CLUS_2           17                171
  CLUS_3            6                182

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           21                120
  CLUS_2           17                123
  CLUS_3            5                145
D60V5, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           11                 83
  CLUS_2            2                 66
  CLUS_3           10                 63
D60V6, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           14                 92
  CLUS_2            3                 67
  CLUS_3            6                 53
D60V7, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           12                143
  CLUS_2           16                145
  CLUS_3           15                135
D60V8, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           11                107
  CLUS_2           16                192
  CLUS_3           16                124
D60V9, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           12                167
  CLUS_2           26                205
  CLUS_3           10                 68
D60V10, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           11                 40
  CLUS_2           26                223
  CLUS_3           11                177
D60V11, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1            7                148
  CLUS_2           22                170
  CLUS_3           14                 64
D60V12, multiclass
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  CLUS_1           12                 37
  CLUS_2           21                167
  CLUS_3           10                178

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           10                131
  CLUS_2           12                128
  CLUS_3            7                143
D61V5, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            7                 87
  CLUS_2            2                 66
  CLUS_3           11                 62
D61V6, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            9                 97
  CLUS_2            1                 69
  CLUS_3           10                 49
D61V7, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            3                152
  CLUS_2           18                143
  CLUS_3           11                139
D61V8, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1           14                104
  CLUS_2            6                202
  CLUS_3           12                128
D61V9, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            7                172
  CLUS_2           24                207
  CLUS_3            4                 74
D61V10, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            3                 48
  CLUS_2           23                226
  CLUS_3            9                179
D61V11, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            5                150
  CLUS_2           22                170
  CLUS_3            2                 76
D61V12, multiclass
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  CLUS_1            1                 48
  CLUS_2           21                167
  CLUS_3            7                181

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           10                131
  CLUS_2            9                131
  CLUS_3            6                144
D62V5, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            2                 92
  CLUS_2            2                 66
  CLUS_3           10                 63
D62V6, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            6                100
  CLUS_2            2                 68
  CLUS_3            6                 53
D62V7, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            7                148
  CLUS_2           13                148
  CLUS_3            8                142
D62V8, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1           10                108
  CLUS_2            9                199
  CLUS_3            9                131
D62V9, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1           10                169
  CLUS_2           17                214
  CLUS_3            4                 74
D62V10, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            4                 47
  CLUS_2           17                232
  CLUS_3           10                178
D62V11, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            7                148
  CLUS_2           14                178
  CLUS_3            3                 75
D62V12, multiclass
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  CLUS_1            3                 46
  CLUS_2           14                174
  CLUS_3            7                181

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           19                122
  CLUS_2           10                130
  CLUS_3            7                143
D63V5, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           10                 84
  CLUS_2            9                 59
  CLUS_3            3                 70
D63V6, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           11                 95
  CLUS_2            7                 63
  CLUS_3            4                 55
D63V7, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           19                136
  CLUS_2           10                151
  CLUS_3            8                142
D63V8, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            7                111
  CLUS_2           19                189
  CLUS_3           11                129
D63V9, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           16                163
  CLUS_2           17                214
  CLUS_3            6                 72
D63V10, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            3                 48
  CLUS_2           18                231
  CLUS_3           18                170
D63V11, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1           15                140
  CLUS_2           18                174
  CLUS_3            2                 76
D63V12, multiclass
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  CLUS_1            2                 47
  CLUS_2           17                171
  CLUS_3           16                172

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           11                130
  CLUS_2            9                131
  CLUS_3            3                147
D64V5, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            6                 88
  CLUS_2            5                 63
  CLUS_3            3                 70
D64V6, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            9                 97
  CLUS_2            4                 66
  CLUS_3            1                 58
D64V7, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            9                146
  CLUS_2           10                151
  CLUS_3            4                146
D64V8, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            6                112
  CLUS_2           11                197
  CLUS_3            6                134
D64V9, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            8                171
  CLUS_2           11                220
  CLUS_3            4                 74
D64V10, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            1                 50
  CLUS_2           11                238
  CLUS_3           11                177
D64V11, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1           10                145
  CLUS_2           12                180
  CLUS_3            1                 77
D64V12, multiclass
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  CLUS_1            1                 48
  CLUS_2           10                178
  CLUS_3           12                176

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           43                 98
  CLUS_2           37                103
  CLUS_3           14                136
D65V5, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           25                 69
  CLUS_2           12                 56
  CLUS_3           18                 55
D65V6, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           32                 74
  CLUS_2            9                 61
  CLUS_3           14                 45
D65V7, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           27                128
  CLUS_2           46                115
  CLUS_3           34                116
D65V8, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           33                 85
  CLUS_2           36                172
  CLUS_3           38                102
D65V9, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           30                149
  CLUS_2           64                167
  CLUS_3           20                 58
D65V10, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           13                 38
  CLUS_2           67                182
  CLUS_3           34                154
D65V11, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           29                126
  CLUS_2           50                142
  CLUS_3           16                 62
D65V12, multiclass
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  CLUS_1           13                 36
  CLUS_2           49                139
  CLUS_3           33                155

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           20                121
  CLUS_2           13                127
  CLUS_3            8                142
D66V5, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            7                 87
  CLUS_2            3                 65
  CLUS_3           13                 60
D66V6, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           10                 96
  CLUS_2            3                 67
  CLUS_3           10                 49
D66V7, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           10                145
  CLUS_2           19                142
  CLUS_3           16                134
D66V8, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           12                106
  CLUS_2           17                191
  CLUS_3           16                124
D66V9, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           12                167
  CLUS_2           30                201
  CLUS_3            5                 73
D66V10, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            2                 49
  CLUS_2           30                219
  CLUS_3           15                173
D66V11, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1           12                143
  CLUS_2           29                163
  CLUS_3            1                 77
D66V12, multiclass
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  CLUS_1            2                 47
  CLUS_2           25                163
  CLUS_3           15                173

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           42                 99
  CLUS_2           33                107
  CLUS_3            9                141
D67V5, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           21                 73
  CLUS_2           11                 57
  CLUS_3           18                 55
D67V6, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           26                 80
  CLUS_2           10                 60
  CLUS_3           14                 45
D67V7, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           20                135
  CLUS_2           41                120
  CLUS_3           32                118
D67V8, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           33                 85
  CLUS_2           25                183
  CLUS_3           35                105
D67V9, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           20                159
  CLUS_2           62                169
  CLUS_3           15                 63
D67V10, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           11                 40
  CLUS_2           65                184
  CLUS_3           21                167
D67V11, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           20                135
  CLUS_2           49                143
  CLUS_3           15                 63
D67V12, multiclass
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  CLUS_1           11                 38
  CLUS_2           52                136
  CLUS_3           21                167

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           22                119
  CLUS_2           11                129
  CLUS_3            2                148
D68V5, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            9                 85
  CLUS_2            3                 65
  CLUS_3            8                 65
D68V6, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1           11                 95
  CLUS_2            5                 65
  CLUS_3            4                 55
D68V7, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            6                149
  CLUS_2           11                150
  CLUS_3           20                130
D68V8, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            8                110
  CLUS_2           11                197
  CLUS_3           18                122
D68V9, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1           10                169
  CLUS_2           26                205
  CLUS_3            3                 75
D68V10, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            5                 46
  CLUS_2           25                224
  CLUS_3            9                179
D68V11, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            9                146
  CLUS_2           23                169
  CLUS_3            3                 75
D68V12, multiclass
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  CLUS_1            5                 44
  CLUS_2           21                167
  CLUS_3            9                179

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           26                115
  CLUS_2           17                123
  CLUS_3            5                145
D69V5, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           11                 83
  CLUS_2            6                 62
  CLUS_3           18                 55
D69V6, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           17                 89
  CLUS_2            7                 63
  CLUS_3           11                 48
D69V7, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           10                145
  CLUS_2           25                136
  CLUS_3           22                128
D69V8, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           17                101
  CLUS_2           18                190
  CLUS_3           22                118
D69V9, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           17                162
  CLUS_2           36                195
  CLUS_3            4                 74
D69V10, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            5                 46
  CLUS_2           35                214
  CLUS_3           17                171
D69V11, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1           13                142
  CLUS_2           32                160
  CLUS_3            2                 76
D69V12, multiclass
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  CLUS_1            2                 47
  CLUS_2           31                157
  CLUS_3           14                174

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           39                102
  CLUS_2           41                 99
  CLUS_3           20                130
D70V5, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           31                 63
  CLUS_2           11                 57
  CLUS_3           19                 54
D70V6, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           38                 68
  CLUS_2           11                 59
  CLUS_3           12                 47
D70V7, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           29                126
  CLUS_2           45                116
  CLUS_3           32                118
D70V8, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           33                 85
  CLUS_2           43                165
  CLUS_3           30                110
D70V9, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           39                140
  CLUS_2           59                172
  CLUS_3           20                 58
D70V10, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           16                 35
  CLUS_2           62                187
  CLUS_3           40                148
D70V11, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           32                123
  CLUS_2           50                142
  CLUS_3           18                 60
D70V12, multiclass
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  CLUS_1           14                 35
  CLUS_2           46                142
  CLUS_3           40                148

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            8                133
  CLUS_2            7                133
  CLUS_3            4                146
D71V5, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            8                 86
  CLUS_2            1                 67
  CLUS_3            2                 71
D71V6, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            7                 99
  CLUS_2            2                 68
  CLUS_3            2                 57
D71V7, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            4                151
  CLUS_2            9                152
  CLUS_3            2                148
D71V8, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            7                111
  CLUS_2            6                202
  CLUS_3            2                138
D71V9, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            5                174
  CLUS_2           10                221
  CLUS_3            4                 74
D71V10, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            6                 45
  CLUS_2           10                239
  CLUS_3            3                185
D71V11, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            4                151
  CLUS_2           10                182
  CLUS_3            4                 74
D71V12, multiclass
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  CLUS_1            3                 46
  CLUS_2            8                180
  CLUS_3            7                181

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           30                111
  CLUS_2           27                113
  CLUS_3           14                136
D72V5, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           17                 77
  CLUS_2            8                 60
  CLUS_3           14                 59
D72V6, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           20                 86
  CLUS_2            7                 63
  CLUS_3           12                 47
D72V7, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           17                138
  CLUS_2           35                126
  CLUS_3           22                128
D72V8, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           25                 93
  CLUS_2           30                178
  CLUS_3           19                121
D72V9, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           25                154
  CLUS_2           40                191
  CLUS_3           12                 66
D72V10, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           10                 41
  CLUS_2           37                212
  CLUS_3           30                158
D72V11, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           18                137
  CLUS_2           40                152
  CLUS_3           12                 66
D72V12, multiclass
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  CLUS_1           11                 38
  CLUS_2           34                154
  CLUS_3           25                163

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           38                103
  CLUS_2           42                 98
  CLUS_3           21                129
D73V5, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           26                 68
  CLUS_2           11                 57
  CLUS_3           20                 53
D73V6, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           30                 76
  CLUS_2           11                 59
  CLUS_3           16                 43
D73V7, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           26                129
  CLUS_2           50                111
  CLUS_3           30                120
D73V8, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           36                 82
  CLUS_2           44                164
  CLUS_3           26                114
D73V9, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           31                148
  CLUS_2           61                170
  CLUS_3           17                 61
D73V10, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           13                 38
  CLUS_2           56                193
  CLUS_3           40                148
D73V11, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           31                124
  CLUS_2           53                139
  CLUS_3           16                 62
D73V12, multiclass
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  CLUS_1           13                 36
  CLUS_2           51                137
  CLUS_3           36                152

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           60                 81
  CLUS_2           22                118
  CLUS_3           10                140
D74V5, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           25                 69
  CLUS_2           21                 47
  CLUS_3           17                 56
D74V6, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           30                 76
  CLUS_2           20                 50
  CLUS_3           13                 46
D74V7, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           26                129
  CLUS_2           29                132
  CLUS_3           56                 94
D74V8, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           21                 97
  CLUS_2           41                167
  CLUS_3           49                 91
D74V9, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           37                142
  CLUS_2           68                163
  CLUS_3            9                 69
D74V10, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            5                 46
  CLUS_2           69                180
  CLUS_3           40                148
D74V11, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1           32                123
  CLUS_2           52                140
  CLUS_3            8                 70
D74V12, multiclass
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  CLUS_1            6                 43
  CLUS_2           50                138
  CLUS_3           36                152

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           33                108
  CLUS_2           17                123
  CLUS_3            5                145
D75V5, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           20                 74
  CLUS_2           11                 57
  CLUS_3            9                 64
D75V6, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           22                 84
  CLUS_2           11                 59
  CLUS_3            7                 52
D75V7, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           14                141
  CLUS_2           24                137
  CLUS_3           30                120
D75V8, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           16                102
  CLUS_2           23                185
  CLUS_3           29                111
D75V9, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           19                160
  CLUS_2           44                187
  CLUS_3            5                 73
D75V10, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            3                 48
  CLUS_2           43                206
  CLUS_3           22                166
D75V11, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1           16                139
  CLUS_2           36                156
  CLUS_3            2                 76
D75V12, multiclass
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  CLUS_1            3                 46
  CLUS_2           33                155
  CLUS_3           18                170

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           20                121
  CLUS_2           27                113
  CLUS_3           11                139
D76V5, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           22                 72
  CLUS_2            3                 65
  CLUS_3           11                 62
D76V6, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           24                 82
  CLUS_2            3                 67
  CLUS_3            9                 50
D76V7, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           15                140
  CLUS_2           29                132
  CLUS_3           18                132
D76V8, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           20                 98
  CLUS_2           21                187
  CLUS_3           21                119
D76V9, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           21                158
  CLUS_2           33                198
  CLUS_3           10                 68
D76V10, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            9                 42
  CLUS_2           37                212
  CLUS_3           18                170
D76V11, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1           22                133
  CLUS_2           28                164
  CLUS_3            7                 71
D76V12, multiclass
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  CLUS_1            7                 42
  CLUS_2           26                162
  CLUS_3           24                164

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           12                129
  CLUS_2            6                134
  CLUS_3            3                147
D77V5, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            7                 87
  CLUS_2            2                 66
  CLUS_3            4                 69
D77V6, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            5                101
  CLUS_2            4                 66
  CLUS_3            4                 55
D77V7, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            8                147
  CLUS_2            6                155
  CLUS_3           10                140
D77V8, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            4                114
  CLUS_2           11                197
  CLUS_3            9                131
D77V9, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1           11                168
  CLUS_2           13                218
  CLUS_3            1                 77
D77V10, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            5                 46
  CLUS_2           15                234
  CLUS_3            5                183
D77V11, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            9                146
  CLUS_2           10                182
  CLUS_3            2                 76
D77V12, multiclass
        clus
vv       20Q LOSS CNV 20Q LOSS WILD-TYPE
  CLUS_1            4                 45
  CLUS_2           10                178
  CLUS_3            7                181

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           36                105
  CLUS_2           16                124
  CLUS_3            6                144
D78V5, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           10                 84
  CLUS_2           10                 58
  CLUS_3           14                 59
D78V6, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            9                 97
  CLUS_2           12                 58
  CLUS_3           13                 46
D78V7, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            7                148
  CLUS_2           13                148
  CLUS_3           43                107
D78V8, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            8                110
  CLUS_2           15                193
  CLUS_3           40                100
D78V9, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           12                167
  CLUS_2           49                182
  CLUS_3            5                 73
D78V10, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            1                 50
  CLUS_2           54                195
  CLUS_3           11                177
D78V11, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1           15                140
  CLUS_2           37                155
  CLUS_3            6                 72
D78V12, multiclass
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  CLUS_1            2                 47
  CLUS_2           38                150
  CLUS_3           18                170

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           42                 99
  CLUS_2           28                112
  CLUS_3           12                138
D79V5, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           23                 71
  CLUS_2            9                 59
  CLUS_3           24                 49
D79V6, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           28                 78
  CLUS_2            8                 62
  CLUS_3           20                 39
D79V7, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           18                137
  CLUS_2           31                130
  CLUS_3           39                111
D79V8, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           22                 96
  CLUS_2           27                181
  CLUS_3           39                101
D79V9, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           23                156
  CLUS_2           58                173
  CLUS_3           14                 64
D79V10, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            7                 44
  CLUS_2           64                185
  CLUS_3           24                164
D79V11, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1           22                133
  CLUS_2           49                143
  CLUS_3           10                 68
D79V12, multiclass
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  CLUS_1            7                 42
  CLUS_2           53                135
  CLUS_3           21                167

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           5               136
  CLUS_2           2               138
  CLUS_3           1               149
D80V5, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1                93
  CLUS_2           2                66
  CLUS_3           2                71
D80V6, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3               103
  CLUS_2           1                69
  CLUS_3           1                58
D80V7, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           4               151
  CLUS_2           1               160
  CLUS_3           6               144
D80V8, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1               117
  CLUS_2           5               203
  CLUS_3           5               135
D80V9, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           3               176
  CLUS_2           7               224
  CLUS_3           1                77
D80V10, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                51
  CLUS_2           8               241
  CLUS_3           3               185
D80V11, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           1               154
  CLUS_2           5               187
  CLUS_3           2                76
D80V12, multiclass
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  CLUS_1           0                49
  CLUS_2           4               184
  CLUS_3           4               184
                           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")
